I was considering how many, if any, new utility parts to involve in the control of allies, though I was thinking of it in a more general sense rather than enabling specific actions. Perhaps I was thinking too closely along the lines of realism, but maybe it could be rationalized in some way (in any case, this isn't a simulation, so good gameplay should always trump absolute realism --if the two end up at odds, that is, which I'd prefer they didn't).
Another terraforming related issue I failed to mention in enough detail is the enemy response, since enemy engineers build walls that have been removed/destroyed from the intended layout of the level, and tunnelers excavate new corridors and rooms that are part of that "intended layout." So if you block a tunnel, for example, an excavator should come along and clear it, but then you could do this in the middle of combat and pretty stop an enemy advance until they get an engineer. Then of course they could also try to just shoot their way through the walls, which could be difficult unless your "temporary walls" aren't very strong, in which case they're not really very useful in the first place... (There's also the issue of letting the AI know what walls it can/wants to shoot, which is somewhat non-trivial for a simple/fast AI.)
Requiring some parts for control could help, but doesn't yet resolve the fact that this terraforming metagame can get a little out of hand (the fact that it could *exist* is good, since that leads to more options, and fun ones, too, but their inclusion may). Perhaps part of the solution could be the enemy response system I've planned to add, whereby the more allies you have and bigger "influence" you start to have in an area, the more resources the enemy will devote to dealing with you. Terraforming could significantly increase your influence since doing things like intentionally blocking off tunnels *is* quite annoying for the general operation of the complex. This is both 1) realistic and 2) balances the game depending on whether you have allies or not.
Edit: Another thought is that building/tunneling could take time, since time is always against you, but then the process shouldn't really be slower than what the same units can do normally, which is fairly quick right now. Slowing that down could help.