In Trek XI we see a Earth space station which is kind of reminiscent of the “Starfleet Headquarters” in Franz Joseph’s TOS tech manual.
http://www.ex-astris-scientia.org/schematics/spacedock-trekxi-wallpaper.jpg
In the movie this station is referred as spacedock. Could spacedock as seen in Trek XI also exist in the Prime universe at the time of TOS, only to be supplanted by the mushroom cloud spacedock in the TOS movie era?
There's no reason to assume that they'd be "supplanted," either.
One of the biggest problems with Trek, both from the standpoint of fans and from the standpoint of those making the shows, has been to treat the Trek universe as being... well... kinda small.
Look around, just down here on Earth. In one country... in one state... hell, even in just one TOWN. There entire "trek universe" is really smaller than that. Just a handful of people, always running into each other at every turn. Just a couple of ships doing anything interesting. Just one "spacedock" at Earth.
I Like F.J's space station concept, though I do NOT accept it as "Starfleet Headquarters." I don't mind it being one of a series of starbase "standard designs" out there, and don't mind one or more of these having a "starfleet headquarters" facility inside (in the same sense that there are multiple "headquarters" operations for the Navy, dependent on which fleet or operational group you're talking about). But there's simply no way to have a spaceborne facility be anywhere nearly as secure and self-sufficient as a planetbound one could be. There are advantages to being in space, but the sort of things you really want from a "headquarters..." not so much.
So, let's just say we have several "F.J" style space stations... with at least one in the SOL system (based upon that design, I'd be inclined to put it near Jupiter, personally).
We know that there are a series of "mushroom" starbases throughout Federation space, with at least one in Earth orbit.
The interesting thing re: the ST-09 station is that it really has more in common with Probert's "space office complex" (albeit uber-over-sized) than with anything else we've seen.
I'd have no problem with it existing in Earth orbit, right alongside a few dozen other facilities. The assumption that there is "just one" is what I find so utterly silly.