Like Tents, bases are meant to be safe places.Some members of your faction could raid a NPC faction, and there wouldn't be a way of knowing who.What would they do if the base was empty at the time?What if you put up an army of mercs, and farm them like crazy?What if it became so bad, that you would have to move bases?What if???
Why should it be one type of a base? A cave could be completely safe, but a bunker could be retaken from the second level.
What about npc faction trying to do town control ?
If you want to make enemies, try to change something.