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If you want to only run one of them at once, you can pursue the Archotech ending. When you complete each of the first 2 stages, your colony is taken over by the computer and you start a new one. It is possible to encounter pawns you left behind at the settlements later in the game.
If you want something like Dwarf Fortress, where you can save a world state, kick out to the main menu, and start a new game in the same world with your old settlement as a faction in the world, that does not exist in any mod I have ever seen.
I think get it, so I would basically have to just create the groups I want to use as colonies in other locations each in their own worlds, have them saved, and then load them in as new factions on the final planet I want to play in, I guess?
EDIT: I can suggest some mods though that can help you customize the factions already planted into your game however, those being:
https://steamcommunity.com/sharedfiles/filedetails/?id=2891975564&searchtext=xenotype+
https://steamcommunity.com/sharedfiles/filedetails/?id=2882785581
https://steamcommunity.com/sharedfiles/filedetails/?id=2649548096
https://steamcommunity.com/sharedfiles/filedetails/?id=2637999346
Wait on the total control mod though, it hasn't updated yet, but the other three are fine.
This is exactly right.
All factions except those created by the player (this playthrough) or the quest system are sort of considered globe-spanning empires that have a ton of settlements and with pretty much limitless populations of faceless masses.
There are some mods that give you a little more control over them (their names, the xeno composition of them, making their "important members" actually show up during certain events), but nothing like being able to load in a base from another playthrough and having them appear as an in game faction.
So you can make multiple colonies, but they all run at once all the time (like if you sent a raid out to hit an enemy base.... You'll run that fight while still being in direct control of any pawns back at your base). They are always all yours, all direct control. There's no auto manage or anything (other than getting a solid late game base running kinda on it's own, but even then, 1) you still stay in direct control, and 2) they won't respond in any way other than what you've told them to do ahead of time)
That arcotech ending follows the same rules. When you "give up" your base, it's not yours any longer. You have no control of it at all. It becomes a generic base controlled by the faction you gave it to. It won't behave any differently than any other base, and that faction won't behave any differently due to what you gave them... Whether you were super rich tribals or glitter tech mechanized society, they'll still use the same fighters and stock the same stuff they always do.