The Top Floor is dummied out, yes. Just accessible via cheating.

Alexis is not the true final boss.
Also, in vanilla Cave Story, Ballos's max HP totals to 3808 (throughout all his forms). The master's is 3108 (as of posting this, since it might change).
Also, there will be cake in a future version, as soon as I sprite it. (Here goes~!)
Oh, and Xyz's forms? Those will now rely on how long you've postponed to battle Xyz.
If you beat the Ghost Dragon Sisters first and then battle Xyz, you'll get his second form (and a "level 1" reset courtesy of Shinica).
(Thus, his second form's attacks will be boosted.)
Also, depending on when you fight Xyz, dialogues change. However, to get deeper into the Top Floor, you have to beat Xyz, Sycor, Irving, Micren, Grialdyn and Valkyrie (and probably Azehr as well).
Azehr and Alexis both "guard" the last starting room treasury, as well - it's empty in version 3, but won't be when Azehr and Alexis's boss fights are added.
And the beach outfit looks different.