1+

Nice so FastTracker 2 made MODs can be played as they were intended.

Yes--agreed.
I just ditched .mod format due to all the unnecessary limitations.
I just use .mptm now, which you should probably use anyway if you're working with MPT!

Should probably also have an option for 100% stereo separation as some people actually want that for their Amiga mods.

The big question is how this would work with panning commands - it could either change the default panning of those channels, or it could forcefully override the pan separation in the mixer for those modules. Overriding the default panning would be more understandable to the user probably, but the interaction with panning commands can be problematic, especially if one user writes a MOD file with 0% stereo separation (maybe even unknowingly) and then adds panning commands to just a few channels, and then realizes much later that the module sounds completely different in another player (or even in another OpenMPT installation with 100% stereo separation). Changing the mixer pan separation on the other hand would do potentially unwanted things to any channels with panning commands that are more extreme than the default 64/192 pan positions.