The first one is weirdly panned, correct me if I'm wrong but I have read somewhere that people did this due to technical limitations on the Amiga.
People did not "do this" (intentionally). It is simply not technically possible to do otherwise in the Amiga MOD format...
And the second would have been corrected?
...and on the other hand, the XM format does not have channel panning but only sample panning, hence everything is just panned to center by default unless you set a different default sample panning for each sample.
I will probably just ask Zalza which file is the original one.
By the way, given a xm file panned this way, how can I make it mono? Using Milkytracker I tried looking for the effect 8 and for panning settings in the instrument view but I didn't find anything.
If you mean MOD file rather than XM, you probably can't as long as Milky plays it in Amiga ProTracker mode.