What was said was that the Rising Stones was built for the Scions, which is easy to fit with the story since the Rising Stones is a separate area.

The arrival of Domans is also easy to fit because you can just move around the NPCs.

New players will never see how Revenant's Toll used to be like, but the growth of Revenant's Toll was never a big issue in the game.

What you're asking for Ul'dah is to have parts of it to be blown away and completely redesigned as part of the main storyline.