A lot of these are already confirmed (temples, resource processing buildings, NPC trade routes between cities). I think resource specialization within cities will be a natural consequence of the way resources are distributed and doesn't need any special restrictions. If a governor of a city in the middle of a desert wants to build logging facilities, let them waste the resources.
As for designated areas, that's up to the governor to decide if they want to designate certain areas of a city to specific activities. Hopefully the town building tools allow the freedom to design and decorate a city as the governor wishes, and it's not as simple and restrictive as placing down a prebuilt town square/crafting area/bazaar/etc.
I don't think player towns will be able to build gateways/portals. We already have fixed locations for these and some limited teleportation abilities. Having too much insta-travel defeats the survival/logistical part of the game.