Hmm...if you have FWE installed, there's a little shack down there if you have alternative starts activated...So that might conflict with it. Although, there's always room for a suburb ontop of Rivet City (I've always wanted to do this, but I have absolutely no clue about the G.E.C.K. at all).
Anyway, for around the docking base thing:
1) You could build a Guard post on the first level off the ground, with a friendly sentry turret looking over the small suburb. You'd also want to build a wall around it, so the Super Mutants couldn't access it.
2) How about a tavern/saloon or whatever you want to call it
3) DON'T build a market, its the suburbs, people would travel into the city to buy everything. This would also show how Rivet City has got so powerful
4) Just for a laugh, I think you should put that annoying guy that always asks for water in a cage, and have the villagers tormenting him