It would have been the main CPU and the chipset would have been "Amiga" in name only as it was a clean break. Any compatibility would have been achieved through emulation.
http://en.wikipedia.org/wiki/Amiga_Hombre_chipset
It would have been much like other console development, each generation a clean break with the previous. A different architecture etc. It's what they should have done, arguably, with the A1200/A4000.
It's all speculation anyway.
I read that the OS was expected to have something similar to "Rosetta"
http://en.wikipedia.org/wiki/Rosetta_(software)I think that a nice project would be to make a version of UAE completely hidden. As Apple said about Rosetta: " "The most amazing software you'll never see".
Windows/OSX/Linux, doesn't matter. Just double click the binary and the program runs on a window.
Sometime ago I got a version of AMOS just like that...