Well, I suppose it does have a consequence. An extremely underwhelming and stupid, circumventable consequence, but a consequence nonetheless. I think what people imagined the Upper City to be makes the story of Larian going from mentioning it in their latest panel shy of a month away from release to just straight up deleting it for full release with no trace of it in the datamines too incredible. I try to stick with Occam's Razor for this one.
Except that the razor says that Larian was/is lying for marketing purposes like they did for other topics.
And its not as if they are above making radical changes to the game in the last minute. See the entire Emperor storyline.