Not really, programs that work with AGA will also work with many of the new Super AGA modes.
Most if not all will work with P96 as well. Anything that doesn't, won't use any new super aga features anyway. So can be used on the AGA implementation
Emulating P96 allows you to use software that already exists, while natami will need new drivers. However I doubt you can use copper to get draggable screens and mid screen resolution changes etc. Plus natami is also talking about h/w 3d rendering, which P96 doesn't have.
What Natami is doing is redefining what the Amiga can do, which will need alot of software work. I'd love to see if, then hopefully someone can figure out how to make it cheap enough.