What he said. An awful lot of things trigger when your first city is founded; for instance, you can't actually assign a player a Project until he has a city, because for whatever reason you're not treated as a real player until you have a city. In my Mythology mod, I had to wait until cities are founded to do this, which caused all sorts of headaches.
You'll also notice this in things like TopPanel, where it won't give values for happiness, golden age progress, culture, research, strategic resources, etc. until you've founded a city, and I don't think there are explicit checks for this in that UI Lua.