Unfortunately those aren't bugs. We're pretty new to the MT-32 and the current solution for the wind chimes was to use the flute and as for the waterfall we just couldn't find a way to express it via the music system that we were happy with. We've been researching into the more complex side of MT-32 programming with modifying patches but it's still early on yet.
An engine expansion we've toyed around with is possibly using meta data to link missing music tracks with the PCM sound effects pack, but we haven't settled on a particularly elegant solution for that idea.
A lot of this is a hold over from the Tandy 1000 3 Voice Sound mode only days where that was what we had so we made due.
What I will say is this won't be the last non-bug fix patch for the Aching and if we find a better solution we'll readdress some of the more questionable solutions to these challenges we're currently employing.