If there were substantial changes to the game's narrative and tone, then I'd definitely assume that's part of the reason why the endings are so rough. I'm not sure the inner city was cut, but there's definitely something strange there with how you can't go into the inner city because the Brain is apparently there... only for it to be deep within the undercity.
In A PCGamer Interview, which references the PC Gaming Show, the upper city was still specifically pointed out as a district in the game
https://www.pcgamer.com/baldurs-gate-3-dev-diary-city-reveal-pcgs-2023/Larian has split the city into three areas—the outer city, affluent upper city, and roguish lower city—all connected in a seamless open world. "You have crowds walking around everywhere," creative director Swen Vincke says. "You can talk to pretty much anybody, and they react to every single thing. It’s very alive in that sense."
And some companions don't seem to have any endings at all?
