This would likely be better achieved by giving building choices for t2 or t3 rather than entirely split districts. (In the harbor case, I imagine any coastal city would want the lighthouse.)
I hope in civ7 they can resurrect an aspect of civ:BE if they want to keep the trade route limit tied to something you can make more of - specifically, the idea that a
city could only accommodate a limited number of trade routes. So in this case, the trade route
slot could come from either district, or a city center "trade depot," or whatever we want, but the CH and harbor could both add
trade route capacity to the city. By cleverly tying things which boost trade route yields to those which boost trade route capacity for a city, you would naturally develop trading hubs in your empire. This naturally opens the door for true trade economic strategies, and for extra historical realism, things like
commercial hub adjacency could itself play a role in trade route yield. Now you have a geographic case for trading hubs!
My one wish for NFP that i know I won't get, is to balance the game such that gold is something you have to work for.

I am sick and tired of Sid Meier's Civilization: Rumpelstiltskin where we just conjure endless gold out of nowhere!