There's a nuance between "Utopia Planitia Fleet Yards" and "San Francisco, Calif.", though. The former could easily be the name of a business, with actual dockyards all over the universe, only named after the one that started it all. The latter with its "Calif." seems to nail it down geographically to a somewhat more concrete degree.
The Defiant and the Valiant came from Antares Ship Yards that explicitly weren't at Antares, but in the Bajor sector, according to the dedication plaques. (Sisko says he worked on the former vessel at Utopia Planitia, which then allows us to think that "Utopia Planitia" is like "Antares" here, not a place at all but a name for a business. Or then the plaques refer to the second life these ships got, after having been discarded as unsuited for their originally intended anti-Borg role.)
As for the "built in space vs. built on surface" issue, both could well hold true. Most (war)ships today are built on land, and then built more after being dropped in water. It might be fairly uncommon in Trek to build a ship to completion on a groundside dockyard, but common to build most of her down there and then to launch her for fitting out in space. We know it's fairly trivial for an operational starship to take off from a planet (or from inside a black hole for that matter), and it might not require much beyond the completion of a hull and installation of power systems and impulse engines to make the ship capable of that.
We never really saw a ship being built in space in any of the shows or movies, FWIW. We saw ships launched on their maiden voyages from space, but that might have been after months of test flights, even the first of which did not start at the construction site but at a test facility to which the ship was first towed or whatever. We also saw ships with hull plates missing, in the likes of VGR "Relativity", but those had low registries and were probably being repaired rather than built.
In contrast, we very much saw NCC-1701 being built on the surface in that one timeline where she was an order of magnitude bigger than in the regular timeline. Perhaps the bigger they come, the better it is to build them down where there's air and ready access to raw materials and perhaps also some helpful gravity...
(Then again, in that timeline, we heard of a ship being built in space, for space, with Scotty having misgivings on whether she could really take off. Which was rather silly, because of course starships can defeat one gee, on one-tenth auxiliary power and after being kicked in the groin by a Doomsday Machine. And of course the ship did take off just fine - much like her cargo transporters worked on people just fine. Scotty's just a big sissy, is all.)
Timo Saloniemi