I like your thinking though. How does this sound?
hamlets, villages, towns: -1 commerce. Farms: +1 commerce. Medium upkeep.
This civic would be a good choice for larger empires still developing and dealing with providing enough food and production rather than more commercially-apt empires. It also fits much better with a specialist strategy, which is fine. Finally, it means plains-dwelling empires (which, to keep everyone fed tend towards lots of farming) wouldn't be as disadvantaged against grasslands-based empires while running this civic.
Yes, indeed. This is very good. Like you said, it also gives a nice option to boost Specialist Economies from the middle-ages forwards (lets face it, the SE starts lagging toward the end-game).
Personally, I also think something should be done about serfdom. How about making serfdom produce +10%

It would also force an SE player to think more carefully about choosing either serfdom or caste system (since caste system has been boosted in BtS it seems like an obvious choice at the moment).