Rebuilders do require supply, so if all surrounding planets are fortified by the AI (and those surrounding command centers destroyed), they won't be able to rebuild the command center (or anything else) on the surrounded planet. I don't think this changes the military aspect of it all - you still have to reconquer your systems if the AI takes them from you. You just get to focus on the interesting (military) aspects of the reconquest, and rely on the game to handle the uninteresting ones.
Actually, if the remains rebuilders claim they still require supply, I'm pretty sure that is a bug. Remains rebuilders can rebuild remains on planets with no supply just fine. They used to require supply, but that was quickly removed once command stations started dropping remains.
Also, the re-fight along the path there is also a military aspect of the reconquest (though one could argue that particular part of the refight is not "interesting").
Also, AI ships no longer just "bum around" forever (or at least for a very long time) on already destroyed planet once everything detected is dead (there were a lot of long lasting bugs where they would just sit around, skewing this particular aspect of this mechanic, but they have been weeded out to the best of our knowledge), they tend to leave for other "tasks" after a while. Which is why I am reversing my previous assertion and I am going to now say that the "surrounding system deny" aspect is actually a pretty significant part to the current balance.
Oh, and for my games, what I often do is keep one remains rebuilder on my remote planets on stand down mode a moderate amount of distance away from the command center, so it won't try to remains rebuild stuff and blow its cover. Then once all the AI ships leave, turn it back on, start the command station, then turn it back off. The additional, auto-built remains rebuilders will then take care of the rest.