In the fifth game, there's a problem with this. You can create a city of mages that hires elementals, or a city of humans that hires undead, and they won't replace the existing cities, but you'll need to input the damn ID, and you'll get cities of the vanilla factions with different units. And even if you add them to the list of random cities, these cities won't appear randomly on maps, but if you add them above the vanilla cities, then the vanilla cities won't appear.
Added 5 minutes later
P.S., didn't they change the buildings? I'm talking about this "city of mages that hires elementals"...