> So if you're looking for reasons that two sub-populations within a country might have noticeable differences today, differing geography is going to be the "horse", while history is more of the "zebra."

This is wrong empirically and providing proof for this is how Acemoglu and Johnson won the economics Nobel. In basically all maps of voting patterns within Europe you can read its institutional history. You can see the border of the Holy Roman Empire in economic and voter data in Poland, you can see the iron curtain in every map of Germany.

If you want one of the counterexamples to your Italy theory, Venice was one of the richest middle-age cities in Italy and it is famously built on water.