i have never come across a device that has different software for different drive formats.
software is soemtimes 32 or 64 bit specific and always PC vs mac specific but that's a different issue.
the only real weakness of fat32 is the 4GB max file size so you cannot store and stream a 10Gb HD mkv moview rip. Even some 1 hour TV shows, in high quality 1080p rips , can go over the 4GB limit.
so long as you first backup any software which is provided only on the stick, you can reformat it different ways for different tests...
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