You can automatically separate by instrument in XMPlay. (under Output in the Options menu tick 'Separate MOD instruments' when using the disk writer) It's not per channel though, so if you spread a chord across 3 channels with the same instrument you'll get the whole chord in the exported track. You could export once with interpolation and then without and mix and match the two sets together.
Personally I'd say only use XMPlay or FastTracker2 to export XMs, everything else still has a few quirks. On the Options/MOD page try experiementing with the pan separation, I have mine a bit tighter than the default.
For .MODs the oldsk00l plug-in for Winamp is good and you can use that with XMPlay as well. (coded by Slammer/Anarchy, remember him?) XMPlay's default still trips up on a couple of things there, even on the PT setting. I can't remember if the free version of Deliplayer2 can write to disk but that was accurate as well.