Yes, you can custom make the BIOS boot from which partition you like. I only know this to be true with the X2-4976.02 BIOS as thats what i use and have changed myself.
EDIT:
Personally i think making everything boot from F would be a good idea, as far as your XBOX is concerned the F partition doesnt even exist. So if there was a new type of modded XBOX checking on live that came out, if you had EVERYTHING on F, with your chip disabled it would look like a standard retail XBOX with no detectable "foreign" files.
