Uhh, that's not all correct, Saga. YES, the Amiga _can_ handle FAT (windows) formated floppies, assuming that you have drivers for this installed. If you don't get these from start, tough luck, because Windows can only read Amiga disks, but not write. This is due to the amiga floppy formating is more complex than the windows format. There are, however, solutions like catweasel... something, but it will cost.
To answer your question, Jacob, a friend of mine has an Amiga 500 with ProTracker 1.1 and it works fine. I'm sure ProTracker 2.x will work, too. I'm less sure, however, about ProTracker 3.x and 4.x, but those versions are ugly and probably not what you are looking for anyway.
If you want to find both old school Amiga sample disks like the ST-xx series and want find out lots of information about the ProTracker series, have a look at:
http://www.protracker.deIt's in german, but you'll probably manage as it's mostly just an archive.
If you have further questions, I'm sure I can assist. By the way, the old school Amigas don't have CD support, as far as I can. You may be able to get a hold of a harddrive, a browser (Kefka says he has one, yeah, he's the friend who had the Amiga) and an ethernet cable to connect between the amiga and to a hub.