Not to justify what they did, it isn't the first time that KINGDOM HEARTS has cut content seen from very early trailers. Remember that ctuscene where Master Xehanort is talking with Ventus in Olympus Coliseum waaay back during the Birth by Sleep days? Yeah.
Again, not justifying it, but a lot of stuff gets revised and checked during development. And I just finished Toy Box and I can attest to that cutscene not being in the game anymore.
And as to Mysterios Tower being playable: yeah, that would have worked in KH2 where Twilight Town led to it, and would feel like another area; now it doesn't. And from the overall narrative, there really isn't a point for there to be Heartless in Yen Sid's entrance anymore.