During the Tribal stage, you control one particular creature, do you not? There was one in the village following the cursor around. But you can still place items and such, and command the others. You are the leader, but unlike a typical RTS, you have an avatar. The equivalent of a king in chess. Would it not be logical to assume that your UFO is a "mothership" and, just as you where controlling a city but could still make vehicles and send them off WITHOUT your direct control, that you could do the same with space fleets?