Well from what I can tell in how the code runs the idea here is that unless the game updates the API the Hivemind/machine consciousness is locked in. Some have found a way to add more points to it so some of the outer ring is used as well but sadly that has not updated after the machine class dropped.

If I was going to update this mod to account for them more I play the game first and list what is underdeveloped and what is overpowered, after that think of how I can take power from the OP items and shift them to the underpowered items.
For the time being, planning and making the tutorial is a starting point seeing as not a lot of people know how to work as a hive mind/machine consciousness. The base game this option disables VIR and has no tutorial to chat about. plus if you think about it what races do we have modded or base that can remotely be a hive mind to start with/ can be fully machine as well.

Pony mod/Pony stuff Changelings comes to mind, they live off of a hive mind and can help add love to the game to boot. (it's not to adult, but the idea here is that they use the love for your mother or girlfriend/boyfriend to farm food for the hive). so far that is not that hard to code for.
Sadly, Red came back and his mod adds ponies as well but is not playing nice with the other two mods. But his adds Anthro ponies and they may be machine as well as normal.

What I am getting at here is that if this mod updates with Mod ID detection you may be able to help support if not extend a sign of friendship to the other mod makers.
I have sent Red a message to see if he can update the mod to better work with others but sadly he shot me down.
sorry if words are miss spelled, spelling is not my best skill.

Here are suggestions for the empire modifier to Hive Mind and Machine Consciousness themselves to add. Can they be put as the modifier for the government type themselves, and not related to civics? I will try to come up with ideas for reworking the existing civics soon.

-Hive mind can have a +5% naval capacity because they are like a swarm and act as one mind and body.
-Hive mind add +10% research speed on Biology technologies

-Machine Consciousness can have -3% ship building cost, because life support systems to support organics are not included or minimal in their ships. They save cost since they don't have to add expensive life support, such as oxygen.
-Machine Consciousness add +10% research speed on Computing technologies

I thought of these ideas for Hive Mind and Machine Consciousness. My rationale for making these values is I want to account for all the bonuses human-like government empires have, but also their debuffs as well. I generally gave Hive Minds and Machine Consciousness civics less bonuses than their human-like counter parts, but also none of the debuffs such as less energy for example because in a Hive Mind or Machine Consiousness there would be no corruption that would account for lost energy credits. Some may seem powerful still, but we have to account that Hive Minds and Machine Consciousness do not get any form of bonuses from Ethics like government empires do so I try to balance it out.

Feel free to add more suggestions or change whatever values I have to something else in order to really flesh out Hive Minds and Machine Empires.

Hive Mind:

Ascetic: Analogous to Enviornmental Economics and Keepers of Harmony and vanilla Enviornmentalist
-20% consumer goods cost
-7.5% food consumption

Divided Attention: Analogous to vanilla Efficient Bureaucracy and Imperial Cult
+2 Core systems
-15% Edict Cost
-5% Ship Upkeep
-5% Tradition Cost from Colonies

Natural Neural Network: Analogous to Technocracy
+1 Research Alternatives
+5% Research speed
+15% Science Lab Build Speed

One Mind: Analogous to vanilla Beacon of Liberty
+20% Unity
-10% Tradition Cost from Pops
+10% State Craft Research Speed

Pooled Knowledge: Analogous to Meritocracy
+1 Leader Level Cap
+20% Leader Experience Gain

Strength of Legions: Analogous to vanilla Warrior Culture and Elite Militaries and Martial Democracy
+10% Army Damage
+10% Army Health
-25% Army Upkeep
+50% Army Build Speed
-25% Army Build Cost

Subspace Ephapse: Analogous to vanilla Citizen Service and War Crafters
+20% Naval Capacity
+8% Evasion Rate
+10% Combat Speed

Subsumed Will: Analogous to vanilla Cutthroat Politics
+1.25 Influence
-50% Governor Recruitment cost
+10% Edict Duration

Machine Empire:

Built to Last: Analogous with Ascetic and Enviormentalist
-20% Consumer Goods Cost
+50% Garrison Health
-10% Army Upkeep

Constructobot: Analougous with vanilla Functional Architecture and Master Engineers
-15% Building Cost
+20% Building Speed
+5% Industry Research Speed

Delegated Functions: Analogous with vanilla Aristocratic Elite
+4 Leader Capacity
-50% Leader Recruitment Cost
+0.5 Influence

Factory Overclocking: Analogous with Meritocracy
+1 Leader Leve Cap
+15% Leader Experience Gain
+10% Combat Speed

Introspective:
+20% Engineering Research Speed
+10% Industry Research Speed
-10% Tradition Cost from Robotic Pops

OTA Updates: Analogous with Imperial Cult
-25% Edict Cost
+10% Edict Duration
-10% Ship Upgrade Cost

Rapid Replicator:
+15% Robot Build Speed
+20% Army Build Speed
-5% Robot Build Cost

Rockbreakers: Analogous to Industrial Economy
+10% Minerals
-10% Mining Network Build Cost
+20% Mineral Network Construction Speed
+30% Mining Station Build Speed

Static Research Analysis:
+1 Research Alternatives
-10% Science Lab Build Cost
+25% Survey Speed
+25% Anonymoly Research Speed

Unitary Cohesion:
+15% Unity
+7.5% Naval Capacity
+0.25 Influence
+5% Fire Rate

Warbots: Analogous to Warrior Culture
+20% Army Damage
+15% Army Morale Damage
+25% Army Health
-20% Army Upkeep

that's going to take time to code, seeing as we have to track down the correct API calls for every data point. I am not pushing down the idea or anything, just saying don't expect it any time soon.
@Dev
The above Idea by NewAgekid52 is backed by me, the upcoming 1.9 patch may re-work some of this due to how the system for 'who owns what' is changing.

There could be several types of hive-minds using the Civic system.

1 - One Mind. Drones are physical extensions of one central brain that processes all information. Drones are not as much as "mindless hordes" as they are simply remote body parts controlled psychically by the Hive Mind.
-2 Research Alternatives
+10% Research Speed
+20% Unity

2 - Collective Consciousness. It's just normal people but with a twist. Everyone is psychically linked to another. Everyone knows each other thought's, feelings and emotions. Over course of evolution, this overlap of thoughts has developed into one Collective Consciousness. This is directly opposite to the One Mind, here the "brain" is decentralized and scattered all around different people that forms it's identity.
+2 Research Alternatives
-10% Research Speed
+2.0 Influence

Another way to come up with ideas for hive minds, is to think of using civics to give them 'personality' a hive mind that is a single mind controlling remote bodies could definitley have one, a collective of linked minds could have an emergent gestalt personality based on the tendencies of the populace. so civics could simply be personality traits, but because they are maginfied over an empire, they have major effects.
You could set it so that there are mutually exclusive 'personality' subgroup civics, Agressive/Defensive, for example
This could even be further expanded with advanced versions of each trait, 'Fanatic personalities' if you will, only one of these could be picked, and would magnify the bonuses, but grant drawbacks aswell
Taking Aggressive (Fire Rate/Speed boost) would then allow you to take Reckless (More Fire Rate/Speed boost, but with an evasion penalty, for instance)

For Machine conciousness, this is a bit trickier, but a similar system of two opposite, mutually exclusive civics with an advanced version of each could be used, perhaps to simulate legacy programming that affected the growth of the machines 'mind'

on Traditions, the most important thing is to go through each of your current tradition groups, and make sure there are no obsolete traditions for Hive minds/machines to pick (for example, happiness boosters), thankfully there is a tradition swap system, so now machines and Hive minds can each have their own version of a tradition

Machine Consciousnesses should have access to the Materialist Tradtitions.

I could see a Mechine intellgance possiple Civic for a "Termnator"-isk one

A choose-at-start-of-game-cannot-be-removed civic (Like Driven Exteriminators, Assimilators, etc) for Machine Empires to make them like the Geth from Mass Effect could be neat. In the sense that they are a networked AI that becomes better the more of them there are together--this could maybe be reworked as more broad 'Exponential Replicator'. Potential mechanical ideas:

Providing adjacency bonuses to each other

Less resources/efficiency the fewer robot pops there are

Increased cost for all influence-related actions (To any amount--stuff like colonizing a new world would take more influence because the network isn't developed there)

Possible influence generation malus?

Fleet bonuses dependent on number of ships

increased build time/cost?

Increased amount of leaders, possibly making leaders in certain categories better/worse the more of that type there are? (Lots of Scientists increases research speed/survey stuff, lots of admirals increases rate of fire/evade, etc.)

Increased consumer goods?

For just Exponential Replicators:
-/+% build speed (of all kinds) on a planet based upon number of pops on it (Maybe make it a ratio connected to planet size, so that way the max will always be a certain percentage)?

Makes pops grow like biological ones, with what type of template (If more than one exists) the pop actually becomes being selectable once it would be fully grown

Huge opinion malus

Disable ALL diplomacy, even with other robot empires?

A very diplomatic/spiritualist Machine Empire would also be fun--something like Spiritual machines on a search for their creators who they worship would be very distinct and something not at all covered in the base game yet. They could maybe not get the opinion maluses other Machine Empires get, but perhaps with the 'negatives' associated with pacifism (Defensive wars, etc.) and having the opinion maluses from OTHER machine empires not liking them--after all, with the exception of the Rogue Servitors, the other Machine Empires seem to have intentionally left their organic creators behind in one way or another, and features like the 'Synthetic Age' tradition imply an outright disdain for organic life, which a 'spiritualist' robot actively seeks out.

A diplomatic hivemind that views other empires (the empire, not its citizens) as people would be nice too:
* +30 opinion to other empires to offset being a hivemind
* +trust / trust growth
* +federal unity

IMPORTANT: there should definitely be a 3rd kind of hive mind: Humanoid hivemind, with psionic focus.

---------------------------------------------------------------------------------------------------

Now, rather than focusing on individual bonuses, let's think about the BIG PICTURE. I ask a few questions:

- what is actually the story here?
- how does a hive mind come into being?
- what choices does it have to make?
- how does it evolve over time?
- how are the 3 hive minds similar, and how are they different?

*** STORY ***

I take inspiration from ant and bee hives, and zerg/protoss/cylons. A hive:

- large populations with a have a fast growth rate
- at the expense of the individuals
- high efficiency and communications
- high efficiency comes at the expense of adaptability
- very united in the same colony, BUT dividing into colonies is a major drawback

------------------------------------------------------------------------------------------------------

*** Hive traditions ***

- there should be many hive-only traditin trees.
- some common to all 3 hives types (bio, robo and humanoid)
- a few are specific to the type
- some mutually excluive paths
- different ones for early game, mid, and late game.

--------------------------------------------------------------------------------------------------------


Translating the above into bonuses and penalties:

*** BONUSES ***

It's hard to decide which should be common to all, unique, or come from traditions, so I'll just put everything here:

>> POPs:
- bonus to unity outpout (15%)
- reduction to unity cost from number of pops (30%)

- 20% growth/build speed
- bonus to pop production (5%, upgradable through traditions - later below)
- bonus build speed (buildings, army & ships) 10%


>> Military:

- bonus to naval capacity 25% (hive military)
- bonus army damage 25% (hive co-ordination)
- bonus to travel speed 20% (organized operations)
- bonus to country sensor range 25% (efficient communication)

>> Civilian
- bonus to survey speed (co-ordinated search operations)
- 1 bonus modification points for robo/bio hives (hive evolution)
- psionic hive gets access to a few psionic traits
- significant (50%) reduction to genetic/robotic modification cost, or 'shroud' cooldown.

- Bonus to "society research" for bio hive
- Bonus to "engineering research" for robotic
- Bonus to "physics research" for humanoid' hivmind
- Those bonuses are 25%, but with -10% reduction for the other two types.


*** PENALTIES***
Just like there are advantages, there are disadvantages. Those should come by default to all:

- colony ship build cost 200% (think queen bees, they're huge and fat)
- NEW colony influence cost 150%
- NEW colony development speed 200% (takes twice longer)
- tradition unity cost from number of colonies increased by 50% (needs tweaking)

- adaptability -10% (except for robots)
- leader lifespan - 20 years for bio, -10 for humanoid
- for robots, ncreased chance of malfunction 25%


----------------------------------------------------------------------------------------------------------------

*** RULERS ***

It's quite boring to have 1 immortal ruler all the time. Hives actually change rulers if the queen becomes old, sick or weak. Therefore I think hive rulers should:

- NOT be immortal, unless they are a robotic one.
- Bio and human hives should have +50 years lifespan
- Robot rulers have reduced malfunction chance

-------------------------------------------------------------------------------------------------------------

I could go on a lot, but only if there is a real interest in my ideas.

I just tried a game and ran it for 60 years. Here I tried to give small buffs to Gestalt Consciousness in 00_ethics.txt so both Hive Minds and Machines can benefit since they don't have the bonuses that regular empires do. I ran it for 60 years observing and haven't noticed the Hive Minds and Machines being too powerful and dominating the relative power charts. So I would like to suggest some buffs for Gestalt Consciousness ethics:

-Made Influence gain to +2
-Added a Resource Output gain of 2.5%
-Added a Naval Capacity increase of 5%
-Added a ship build reduction time of -5%

I think these changes can make sense for Hive Minds and Machines Consciousness. The Resource Output is not all that much, especially when compared to 100% happy pops gain +20% from happiness, but it is nice to have since I'd think both robots and happiness-unaffected hives don't worry too much about their needs such as rest and recreation compared to normal people, so they can work longer and a constant rate at higher capacity, but don't get motivated to excel like normal people do. The naval capacity and ship build time is due to their ability to be connected to one another and coordinate ship manuevers better due to being connected whether by computers and machines, or by their psionic hive link to act like a swarm. A ship build reduction time due to that they are like a swarm, and machines can build it faster due to not needing to put life support systems like organics need.

Feel free to edit it however you see fit. Here is what I did:

--------------
ethic_gestalt_consciousness = {
.............................................................
country_modifier = {
country_resource_influence_add = 2
country_core_sector_system_cap = 4
pop_resource_output = 0.025
navy_size_mult = 0.05
spaceport_ship_build_time_mult = -0.05