I was feeling smart and tried that, they trash the place and take a massive dump in the middle of the living room
That sounds like a way to conveniently remove a colony I do not want anymore but cannot abandon for some reason. My primary colony has not built up that far yet, only enough that I cannot abandon it (but still small enough for sat bombing to obliterate).
I would not use the lesser cores as governors, but to buff markets like other items do. I suppose Hegemony might inspect such a colony too if I use them for that purpose.
I wonder if Alpha cores will try to refuse removal if plugged into a market instead of an administrator. (If I plug in Alpha for one market instead of for the whole colony.)
I think I saw rogue AI just means it can't be removed, if that's it it isn't much of a penalty(alpha AI is the perfect admin).
I think alpha AI goes rogue if you remove the core. You do not get the core back, but you can use another administrator.
If I want to deal with Hegemony, then sure, alpha cores would be fine. I am not ready to have Hegemony be a thorn-in-my-side yet, especially since they are handy neighbors to help bootstrap my colony. (I take frequent trips to their easternmost system to get supplies and fuel, my colonies do not produce enough.)