I tested the three:
Tolerance16 produces the exact same result as the normal version.
Tolerance25 and DontKeepRatio both create a black border too, but the actual playing area is larger, especially in DontKeepRatio. None works as actual fullscreen, though and both mess up the aspect ratio.
I'm wondering, however, if this is worth trying to fix, since the C++ build is coming up and that version may as well replace the MMF2 one.