It's standard operational procedure. Unfortunately. I'd like to see some concept of owned territory covering those holes that let anybody through, but nothing like this seems to exist. And the idea of a potential enemy creating a nice fat city in the middle of your territory is annoying.
But there it is. I don't think this is going to change, and we'll live with it. Hopefully, somebody will be able to mod the cost of pioneers (and of arcane monoliths) at some point to make them much more expensive yet something the AI will seriously consider.