@FearTheBunnies i think i got a bug regarding this mod affecting spawning behaviour in my campaign (lwotc, mod jam). also, your mod aswell as all the other mods were installed and enabled when the campaign was started (at 4th jan 2024) (i took this mod in since it was a requirement for mocx class phantom). and yes, the behaviour of this issue existed on 4th jan already.

issue: basically, depending on mission type, mocx fills with advent/other soldiers.
example:
1. hack workstation in advent train - 2 mocx have their original class, all others are (unupgraded) advent troopers. when pod is triggered, all move into cover except the 2 mocx soldiers (sitrep says: "mocx squad")
2. rendevouz & 1 other mission type (normal mission type but forgot which) - 2 mocx soldiers have their original class, all others are pulled from the collector drone/vanguard/assassin pool (mods from NightNinja54)
3. assault facility/liberate region - all mocx spawn as their respective classes, as i would expect.

however, when i launch the exact same mission (hack adven train workstation) from geoscape after disabling your mod, mocx spawns with their normal classes with 2 minor changes;
1. all mocx hq upgrades are "lost", i.e. mocx tech being as if they just launched
2. sometimes, 1 or 2 advent soldiers are in the pod. probably because phantom/zealot mocx unit mods have been disabled too.

things i tried to edit in your config files (except point 0 below) to solve this issue (but doesnt solve the issue)
0. remove mocx rookie sitrep from original mocx/edit that entry in the original mocx mod to make sure it's not this rookie sitrep which is triggered & also giving mocx a giant pool of soldiers/replenishment/and so on + make sure they replenish for a month.
1. removed any of your adjustments from alliesunknown.ini, bossdata.ini, csa.ini, darkcusto*.ini
2. in darkxcom.ini, removed all except: MaxRecruitmentBonusRanks = 3, bDarkClassesAllowBrigadierRanks = false, +bVerboseDebugLogging = false, [DarkXCOMRedux.XGCharacterGenerator_DarkXCom]
// This needs to be TRUE so that Customizer+ manages ALL the outfits
UseEntireAppearance = true; (also the // entry isnt the cause of the issue)
3. xcomeditor.ini only +ModPackages=FTBMocxUsePoolClass exists
4. in engine.ini commented out all 3 entries in [Engine.Engine]
5. game.ini only has DLCIdentifier="FTBMocxUsePoolClass", +RunAfter=DarkXComRedux left
6. gameboard.ini has both MocxSpawnAsExalt set to false and the two X2CountryTemplate

as for console outputs, some lines which might be helpful evenutally (note: your mod and the sitreps in the mocx mod are back to defaults here):

with your mod enabled:
[0023.77] Warning: Redscreen: X2SitRepTemplateManager::FindSitRepTemplate(): Unable to find a template with DataName: MOCXRookies
[0104.82] Warning: X2SitRepTemplateManager::FindSitRepTemplate(): Unable to find a template with DataName: MOCXRookies
[0149.52] DarkXCom: Dark XCom: mission has MOCX SITREP, adding.
[0149.52] DarkXCom: Dark XCom: Could not find valid unit. (this line appears 60 times (which is the amount of barracks mocx has in the current test setting) and also the darkxcom line "finished making squad" doesn't appear after this.)
[0150.07] LWTrace: Tactical Tag on mission: SITREP_MOCX
[0226.50] DarkXCom: Creating new MOCX reinforcement spawner.
[0226.50] DarkXCom: Creating MOCX squad reinforcements
[0226.51] DarkXCom: Altering MOCXDummiesX4 pod to represent actual MOCX squad
[0226.51] DarkXCom: Dark XCom: we are at tier _M2
[0226.51] LWTrace: PostReinforcementCreation called. Current Force Level: 15

for comparison, this is what the respective console lines look like after i disabled your mod (rest stays the same: load geoscape savegame, start mission which has to be started since infiltration time is up, round 1 throw grenade, end turn):
[0023.15] Warning: Redscreen: X2SitRepTemplateManager::FindSitRepTemplate(): Unable to find a template with DataName: MOCXRookies
[0126.60] Warning: X2SitRepTemplateManager::FindSitRepTemplate(): Unable to find a template with DataName: MOCXRookies
[0169.09] DarkXCom: Dark XCom: mission has MOCX SITREP, adding.
[0169.09] DarkXCom: Added following MOCX soldier to squad: Aliaksiej Matskevich
[0169.09] DarkXCom: Added following MOCX soldier to squad: Ayat Behom
[0169.09] DarkXCom: Added following MOCX soldier to squad: Farid Fares
[0169.09] DarkXCom: Added following MOCX soldier to squad: Ross Harrison
[0169.09] DarkXCom: Added following MOCX soldier to squad: Louis Cadet
[0169.09] DarkXCom: Added following MOCX soldier to squad: Sote Exoxus
[0169.09] DarkXCom: Added following MOCX soldier to squad: Hoda Isra
[0169.09] DarkXCom: Added following MOCX soldier to squad: Hwang Han
[0169.09] DarkXCom: Dark XCom: Finished making squad.
[0169.65] LWTrace: Tactical Tag on mission: SITREP_MOCX
[0244.37] DarkXCom: Creating new MOCX reinforcement spawner.
[0244.37] DarkXCom: Creating MOCX squad reinforcements
[0244.37] DarkXCom: Altering MOCXDummiesX4 pod to represent actual MOCX squad
[0244.37] DarkXCom: Dark XCom: we are at tier
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkGrenadier
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkSpecialist
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkRanger
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkPsiAgent
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkSniper
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkReclaimed
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkZealot
[0244.37] DarkXCom: Dark XCom: found soldier class - DarkSpecialist
[0244.37] LWTrace: PostReinforcementCreation called. Current Force Level: 15

also quick question: does your MOCX Class: Phantom work without this mod too? (assuming i don't care about invisible weapons and such things - asking since phantom has this as dep)