Hmm, so surely all they have to do is provide the flash memory unformatted, leaving formatting as an exercise to the user? I assume these are just like floppy disks (which incidentally also tend to come pre-formatted with FAT FS), and don't care what format they have - so on an Amiga you could format them with FFS.
I don't think you're grasping all the implications of the raw format being licensed. That means that it's
impossible to write a non-infringing FAT filesystem, because regardless of how it's written, the bits on the disk (ie what is being licensed) must be the same, otherwise it's not a FAT disk. This affects the amiga because if one does not pay the license, then the only way to share files with a PC is a network of some kind, or a writable CD.
That said, I'd gladly pay an extra quarter for OS4 if it means I won't have to worry about this. People like Hyperion and Genesi aren't going to be hugely affected, especially if the license is a once-only, per-copy fee for the driver. The ones who are royally screwed are the ones writing open-source filesystems (eg the AROS crew).