Oh my damn. This is a phenomenal tool. I am so pleased to have found this!

One question. I have a couple of errant villages that are desperately in need of gates from an outer wall to the city proper. Is there a way to place new gates?

Also, I noticed that my city doesn't come up in the Overworld when I generate it. Is there a way to have that happen?

There is currently no way to add gates to an existing city, but you can request more gates for new cities if you feel like there aren't enough of them get spawned (Generate > Roads).

Could you share a link to a city that doesn't come up when its "Overworld" is pressed?