it could maybe add some more variety if both sides (byz&rum) are ai. but since i've hardly seen rum-ai grow strong it would need some other significant changes to make them somewhat relevant. starting with only one or 2 barb-conquered citys would make them incredibly weak.
but as soon as either byz or rum are player-controlled it would have to be changed completely. as byz it would be far to easy to completely avoid any rum in anatolia (rum is already not that much of a problem to deal with). starting as rum with only the cities being conquered by barbs would be pretty annoying imo.
thats actually the basic point about this "making it more historically correct". you still gotta keep it somewhat balanced and interesting, no matter which faction is human and which is ai-controlled. it's possible do add some minor changes if a side is human-controlled, but in this case there would need to be some radical changes. anyway, for me this issue, the question which units/cities should flip in which case, looks more like eye-candy to me than something that would actually bring some real benefit to the game.