Good question. The way I'm interpreting it is that the minutemen could potentially be this up for grabs faction that the SS can influence.
The more I think about it, it'll probably be a fork in the road sort of decision. So, we'll tackle the problems as they arise. If we side with the BoS for example, we'll probably find ourselves at odds with the Institute at first, and then we'll deal with the Railroad when the institute is dismantled - or vice versa.
As an aside, I'm curious what the Community Organizer achievement entails. Does it tie in with settlement building in anyway?