Specifically, they are both playing the original Quake soundtrack for the main game, instead of their own music tracks. I've tried to fix this but can't figure out which .ogg files in the MUSIC folder are meant for each expansion, and also what determines which ones are used when the game boots up.

Anyone more knowledgeably about this that could lend a hand please?

Yeah, I've noticed this music bug as well. I've fixed it by using the Yamagi mod for Q2. To play the original Q2 music with Yamagi, make sure to copy the music folder to the \baseq2\ folder so the path becomes Quake II\baseq2\music. Each OGG file must be renamed to 02.ogg, 03.ogg, etc. But in order to play the Ground Zero (Rogue) music, tracks "12 - 21" will have to be renamed to "02.ogg - 11.ogg" or Yamagi won't be able to play them.

Update:
I've just realized that this question may be for Quake 1 and not Quake 2. If that is the case, maybe this thread can help you out.

Sorry for bursting in a discussion rather than making my own but you seem to have just the answer i'm looking for...

I already download 20 named all track( from 2 to 21 ).ogg but the source were i download them claim in plural: "Quake II + Mission Packs Soundtracks - ogg".

All fits except The Reckoning, i thought some of the files would go to the xatrix folder for it, please explain this to me, as far as i know from yamagi's page from instructions says one can install audio files under music in /baseq2 /rogue and /xatrix and now i'm about to solve it thank to your comment, just a little more piece to the puzzle though

The Reckoning reuses music from Q2 and Ground Zero. Based on youtube uploads of orginal soundtracks I guess that the reckoning soundtrack consists of tracks 9, 13, 14, 7, 16, 2, 15, 3, 4, 18 from Quake II/music directory