i've come to conclude that the internal universe(s) are a grid of places that are not in san andreas, like the resturants, clothing srores, cinematic sets, special mission buildings, etc. all the places you teleport to when walking into yellow marker, when doing a mission, or the places you see cj acting out a scene.
the abyss i have come to believe is san andreas, but all is invisable except sections that you would see from the windows of places you can go inside that are nowhere else(like the atrium). when i was exploring the abyss, i found a section of downtown los santos. i accidently went into the attrium and when i went back out, my map sid that i was somewhere in the south-eastern part of the ocean, when i was accualy in commerce. i went back to the atrium after i loaded, i noticed that when i looked out the window, i saw only the same section i found in the abyss(there was even ppl walking on invisable ground)