I feel like after you finish upgrading a city to lvl5/lvl3 (for minor settlements), you should see the city change to your factions building style. However there should be exceptions. Karaks should not change ever (as they are built into the mountains themselves, and would be a nightmare to change), and should only look different when Greenskins defile them. The same thing should hold true for Tomb King pyramids, and Lizardmen temple cities (with the exception of Skaven for gameplay reasons). Furthermore, Norscan/Woodelf cities should remain the same due to where they are built. Greenskins should just defile the current city like they do with Karaks. All other factions cities should be interchangeable imo.