IMO, it's because of (1) writing choices and (2) due to the limitations of the game graphics (we get part of one big city rather than multiple cities or settlements), and the city being in the title and at the endpoint of the game, they just tied everything back to it. From a writing standpoint, IMO, the plot is weaker than in some other crpgs because it's trying to juggle every companion having main character syndrome. (I dislike the origin character thing and think the best crpgs have a set main character, though, so that's my personal opinion).
I don't think they would have had to actually render Neverwinter or Waterdeep in order to have the companions come from there. But yeah I agree 100%, the Origin mechanic was a non-starter from the word go. If it's supposed to be BG3, why are you trying to force Divinity Original Sin 2's set up into it? I heard they originally were going to kill extra companions off after Act 1 just like Fort Joy too, which is why the party management is so scuffed. Because the system was originally made when you didn't have to swap people in and out.