The difference between PAL and NTSC playback is not just in pitch - it's also in playback tempo. So the modules still play correctly. At that point, it's probably just a matter of taste and not a compatibility problem.
Testing with WinUAE further shows me that NTSC Amigas do indeed play slightly faster tempo-wise, but the samples still play ever-so-slightly higher than the pitch proportionally to the tempo, leading to the same problem that's happening with MilkyTracker and the drumloops (slightly hiccuppy sound, and the clicks), but less severely. I've attached a recording comparing both PAL and NTSC modes in WinUAE and how they affect the drumloop's hiccupyness and clickyness. So while playing PAL Amiga modules on an NTSC machine definitely is more correct in its playback than PAL modules in MilkyTracker, it's definitely not completely compatible.
Basically what I can deduct is that PAL .mods on PAL-adjusted players play fine, PAL .mods on NTSC Amigas play ever so slightly faster in pitch relative to tempo, and PAL .mods in MilkyTracker is just really off in regards to its tempo-pitch relationship, taking the issues of PAL mods in NTSC Amigas and exaggerating them. I'd still feel it would be worthwhile to add an option for PAL pitch, so MilkyTracker can play back MOD files correctly without the pitch-tempo mismatch it currently experiences.
