Those screenshots are indeed not so clear, but I see your "problem".
For the first 2 pics (Greco-roman and Far-East citysets) I didn't alter a thing. If you start a Warlords game you'll notice that in the Ancient era those sets have mixed structures as well.

Actually, what you see is what was intended in the third and fourth pic, because there's not many new structures to work with I mixed existing civ structures with new graphics in the Ancient and some cases Classic era too.
For the last pic (Persia I suppose?) I'm more or less waiting on Prestidigitator to get moving and work on Mesopotamian cityset which I could implement on Persia and Egypt. So there the first 2 era's will show the european structures and then change into the middle-east cityset in medieval -and renaissance era's.
Okay, since when I released this minimod, a new .dds file was released for the mesoamerican cityset. I will incorporate this one in the mod when I find the time and the stone houses will probably only show up in the ancient era then.
The main reason why I do this mixing is to avoid cities with too many similar looking houses in it. One cityset per artstyle simply isn't enough to keep things progressing throughout 4 era's. With 2 citysets it is doable.
To recap:
Greco-roman: Ancient era mixed buildings, then pure greco-roman until Industrial Era
Far-east: same as above
Europe: different sets/era. The Classic era is a bit mixed with the medieval cityset.
Viking: ancient era is mixed with european ancient cityset, the classic and medieval era are pure norse. Renaissance goes back to the European renaissance cityset.
Meso-american: currently first 2 era's mix with European ancient era cityset. Medieval and renaissance are pure meso. This will be changed a bit when the time comes.
Fertile crescent: first 2 era's come from the european ancient cityset. I simply have no unique graphics for these era's. Medieval -and renaissance switch to Middle-east for obvious reasons.