Yeah there's something legitimately wrong with how the SNES Doom music is programmed, some of it feels like those really fucked up Guitar Pro tabs you can generate by importing midis at a slightly off tempo to the original song. I don't really care for most of the timbres (I'm guessing this is the right term to use, as I'm not very familiar with how the SPC-700 deals with music samples) used for the drums, guitars, and... just about every other instrument.
As for the 32x, IIRC Doom's terrible music was all written very lazily in M68K assembly using a horrible sound driver and then 100% of the digital sfx are offloaded to the 32x's two (three maybe?) PCM channels with literally no software mixing whatsoever. In other words, the music is just bad because it was extremely lazily programmed
Kind of fitting that all the M68K assembly written for the 32x Doom music is stored in what are affectionately (and probably intentionally) dubbed ".gas files"