Currently there are only two checkboxes regarding MOD playback: Protracker 1/2 Mode and Amiga Frequency Limits.
The Protracker 1/2 mode disables panning commands, enables Amiga frequency limits, changes the way samples loop, and allows samples to be changed without a note next to it. However, I have come across some MOD's that use both the Amiga features and later features (such as both on-the-fly sample changing and panning commands.) I think that these playback options should be given separate checkboxes to allow said MOD's to be played back more accurately.