I'll echo what others have said here - Blitz is far more flexible and advanced, and has so many advantages against AMOS that it's almost a non-brainer. If you ever want to do anything system-friendly, AMOS gets tricky quite fast. Blitz is still developed now, and there is a rather excellent set of includes now bundled with it which cover things like MP3 handling, AHI etc. If you're good with assembly it supports that (you can even include PPC assembly for PPC-equipped machines).
To answer your question, yes, Blitz supports CD32 and 2-button controllers, and the 4-player adaptor for the parallel port IIRC. And with the bundled includes it has most of the OS constants and scructs, so you can use OS calls relatively easily.
Check out
HD-Rec for an example of system-legal Blitz software.