I question the "alternate univese" concept. There are just too many references to all be easter eggs. Love Fist are mentioned multiple times, the mansion, Lazlow saying he used to work on Chatterbox, the TVs that have images from San Andreas on them, they are found all over the place. I think this city is in the same universe, it just "replaces" the other city. So the other city never actually existed. Meaning that, while canon, Claude and Toni's missions took place in this city. This is just IMO, I understand no one else takes this view. And despite the graffiti, I think Claude is still alive. Cause you can't kill him, he is just too good for that, and he was too young to die of old age. (That last bit was all IMO, of course, however ridiculous MO is )
It's a game, not something that was created out of nothing, it's obviously gonna have a lot of references.