For only a moment, it was nice to think that perhaps the presence of the city-ship in the Bay was a Toobworld reason as to why the city was chosen to be the home for Earth's Starfleet headquarters - keep such a prize close to a base of operations.
Unfortunately, such musings lasted only a minute, because the 'Stargate' franchise long ago cast itself off into a different TV dimension than the one in which the rest of Earth Prime-Time existed. We know this from the episode which introduced William Devane as President Hayes.
It's a basic Toobworld tenet that the President of the United States in any TV show must reflect the actual POTUS. Too many shows are going to make references (or jokes at his expense), and they can't ALL be tossed off into their own dimensions. Where's the sense in even playing along at home if everybody has their own dimension?
That the Earth as seen in the 'Stargate' dimension seemed to have weaponry and aircraft far more advanced than we do in the current timeline wasn't a deterrent. Like the Valiant, which belonged to UNIT, in 'Doctor Who', all of the aircraft seen battling the Wraith ships in the finale over the skies of Earth could have been kept secret from the general populace of the planet, even from other branches of the military. This would be why even their prototypes were never mentioned in episodes of 'Pensacola: Wings of Gold'.
But Henry Hayes throws the show's timeline off-kilter from the rest of Toobworld. And the blame for that can probably be laid back in the second season of 'Stargate SG-1', when four members of the SG-1 team went back in Time to "1969".
Here's a relevant bit of information from the Gateworld Wikia:
The time travel theory that is implied here (and in many science fiction shows) is that alternate universes exist for every moment of time. SG-1 could travel into its own future because somewhere, in some dimension, all the intervening moments had occured. On some "version"of Earth it was decades past 1999. You would not "blink" out of existence if you went back in time and killed your grandfather, because you would be travelling to a different version of reality. The reality from which you come would remain the same (though getting back to it after altering the past would be a problem).
The paradox aside, it should suffice to say that altering the past can have tremendous ramifications on the future.
Although in the grand scheme of things O'Neill and his team did not change anything, just by hitching a ride with those hippies to Woodstock may have been the significant factor. What if, by traveling and talking with the SG-1 team, one of the hippies was influenced not to vote for a particular candidate in some future election; perhaps even be convinced to actively campaign for some other candidate, which could lead to a groundswell of support which altered the state of politics from the established timeline?
Whatever happened, the SG-1 team returned to a future they didn't know. It could be they never realized it; maybe the significant alteration didn't occur until Henry Hayes was elected President.
But whatever the case, I think General Hammond watched his team go into the Stargate during that solar flare, but he never saw them return. Instead, they found themselves in a parallel dimension.
So whenever we've seen scenes set at the San Francisco headquarters for Starfleet in any of the shows in the 'Star Trek' franchise, we can't imagine the city-ship of Atlantis parked just beyond the Golden Gate Bridge.
But at least we can say that the 'Stargate SG-1' series began in the main Toobworld, and that most of the characters we knew before the "1969" episode do still exist there. But O'Neill, Carter, Jackson, and T'ealc are no longer on Earth Prime-Time, and every character we've met since then are from the same alternate dimension where they found themselves. (As are the doppelgangers of the characters they once knew.)