In addition to the first part of my post... I suppose that given the "made with modplug" flag is actually not set (and thus the proposed version checks won't be applied), the "extended filter range" flag and/or stereo samples (not all files in the same soundtrack use extended filter range, but they have the same issue) could be used as an additional indicator for legacy ModPlug files, perhaps?
This should probably not happen if any of the recent MO3 2.4.1 additions are found, though. It should probably also not be applied to any of the other ModPlug hacks, because these already have a well-defined behaviour.
The only alternative I can think of right now would be applying this quirk to any MO3 files with a version older than 5, as those would most likely have been created and verified during a time that a buggy XMPlay version was around.
I can't think of any other heuristics to make this file play as intended after fixing this playback quirk. What do you think?