LemmyM:
AFAIK, the AI would behave the same, because it works on a case-by-case basis and not as a 'look at the empire as a whole' thing. But I think I know what you mean...the AI on one Quadrant map wouldn't know that it also existed on the other Quadrant map...they'd be the equivalent of Neutrals stranded in their own system.
Either way, thinking about it, I have enough problems securing 250 systems as is.
Try conquering without glassing worlds...it rilly drags it out and forces you to keep supply lines!
zen