I guess I got my GUS MAX too late to ever try it with SC2.
The pitch SC2 plays at in DOSbox seems to agree with the pitch Modplug Tracker plays at, and what UQM plays at, so I'll assume the 3DO version is just a little funky.
Another funky thing about the 3DO version is its stereo. It seems to put channels 1 and 3 to the left and channels 2 and 4 to the right, while MOD players default to channels 1 and 4 to left and 2 and 3 to right. I think the MOD players are right, as far as the way things used to be back when these ancient MODs were actually made