I think this sounds like a nice mod idea. However why so worried about only one map tile per settlement? It's a huge improvement even if you just build smaller versions of the real cities, anything in that direction is better than the standard cities they have now IMO. A question: will these modified cities also have buildings appear when you build them? For example in Athens, should parthenon be there even if you only have a shrine in the city? IMO the best way of implementing this mod would be to change what's in cities from start so that Athens for example starts with temple or large temple and so on.

I also wonder if it's possible when making Carthage to make that cool dry dock change as the port of the city is upgraded?