What is cut content and isn't is frankly irrelevant. Whether or not Karlach's endings were what the writers intended or are a result of the cut Upper City (which I still don't really buy) doesn't change the fact that I'm disappointed with the ending's current state, hence me joining this thread to begin with.
Maybe Karlach did have a quest in the Upper City, maybe not. Maybe we'll see the Upper City in a future Definitive Edition. maybe not.
Either way, the tools that the game provides should give us an option to repair the engine. If Larian wishes to go the "sometimes you get dealt a bad hand of cards and that's life" route, that is their right as the writer of the story, but I'm also well within my rights to complain about disagreeing with it and wishing for a better outcome.