I've found one major use of all this settlement/base building. At some point you get the ability to build artillery for all your settlements (you get it after a certain quest chain). This is quite crazy stuff, it's like having a pocket airstrike/nuke. I wiped a few encampments around a few of settlements out with this, you toss a flare into a camp and your closest settlement will bomb the crap out of it.
So theoretically if you open up as many settlements on the map as you can, and add artillery to them, you can use that to bomb in a radius around it and in turn cover large parts of the map. Obviously won't clear underground/inside, but does help with outside enemies.