I gave that "D2 - Music 03" demo a try now... honestly I'm not entirely sure what to think here. The clicks sound very dominant in that part, while you could argue that Echo Drops plays a similarly low-pitched note and matches better with Breath Noise.
On that "D1 - Level 14" example take a look at the panning of Breath Noise/Fl. Keyclick and Gt. Fretnoise. It's identical. I'm not saying it proves anything, but Breath Noise and Gt. Fretnoise could be considered identical in "purpose", so the identical panning would go well with that theory. Although on the other hand Fl. Keyclick does seem to go well with the drums...
Now for my idea... the game supports the Gravis Ultrasound. I don't know if it utilizes the card in a non-GM compliant way or not (and I'm not familiar with it at all, either), but maybe it'd be worth taking a look at what patches it uses on a GUS? Same goes for the AWE actually... at least in Duke3D the AWE mode does yield different results on an AWE card than the GM mode (i.e. direct access vs. going through MPU-401 emulation), so the arrangement might be different. Again, this will not prove anything (nothing 'cept for contacting the composer will, or equivalent direct sources of information), but all of that could give hints as to what the composer actually had in mind. As in, if he wanted to have click percussion on the AWE (which has only Breath Noise at that position) maybe he would have used something on the drum channel instead, to give an example.
But on a further note, maybe I'm thinking way too much into this and they didn't give a flying f*ck about how it all sounds... after all, in Blood all you get is Pianos when starting the game on Yamaha.