While experimenting with the MO3 compression ratio, I found two little edge cases in MO3.exe... The attached example file uses all possible 255 instruments, but instrument number 255 ends up as instrument 0 (i.e. no instrument) in the imported pattern data. In fact, XMPlay seems to have the exact same bug.
There is also another peculiarity in the "usage" column of the instruments. Each instrument should be used equally often, but starting from instrument 173 onwards, the usage number is 64 lower than with the previous instruments. Since XMPlay gives up trying to calculate the song length of this file (which should be just one long song with no subsongs, but it shows up as two subsongs), I guess it's related to that.