Well, building an ocean liner on a mountain is bad because it will be very difficult to move. It's not the same as building a starship on the ground. A starship can quite easily go from ground dock to orbit. Flying saucers don't have mobility issues.
There's no real advantage to be had from having it built in orbit, unless you are building them in bulk and don't have space on the ground. But Trek ships have never been built in bulk numbers.
I know how strong fan assumptions can be, and how they often override real-world happenings, or even canon itself (NOOOO). But I really don't have a problem with them building it in San Francisco like the plaque says.