I'm looking to rewrite SNDH tunes into other formats, usually my ears get the job done well enough but they can only get me so far.
So yes, is there a player out there that allows separate playback of each of a SNDH's channels - or YM at the very least?

You could use JAM Player on Windows/WINE.

Something like STj ?

Jep try JAM player by CreamHQ!

Winjam is very good, and you can also mute the channels in STj if you want to work on the Atari. But yes, WinJAM is certainly the easiest.