In a lot of the profession!AUs (though I can't recall if I ever read cesare's in particular) the business can work for me as the altantis!stand-in - the bakery or coffee-shop or design firm or whatever, even if they don't carry over the name. Having something that they all come together around to protect and build is close enough. I'll also buy a fic that doesn't necessarily have that but has a hint that Atlantis is waiting for them somewhere else - there have been a few fics where, say, John has a strange artifact he bought at a yard sale that lights up when he touches it, or Rodney drops hints about a secret government project that's trying to recruit him, or Lorne once encountered a life-sucking vampire in the desert, or whatever, without it ever being a central part of the story, and that's enough for me. (I realize that not everybody feels so strongly about the city as fundamental to the story though.)

Also I think what you mentioned about Boom Boom Room is key - if the AU only really features two or three canon characters, then I buy it as an alternate-timeline AU, if you know what I mean? That they still live in the same world, but things happened differently in the past and these two characters just chanced to meet up again, and you can diverge a lot more from the show's core and have me buy it. Whereas if you're recasting almost everybody, especially the non-Earthborn characters, then I want it to be more about re-telling the same stories in a different way, and I want Atlantis to be part of the story.