@Dinierto Did you get an answer on this? I have the same problem.
I can't even get sound/cdtracks to get picked up by Darkplaces. Which folder did you put that within - mine is sitting in /home/pi/RetroPie/roms/ports/quake/id1/sound/cdtracks - but I've tried /home/pi/RetroPie/roms/ports/quake/id1/id1/sound/cdtracks and /home/pi/RetroPie/roms/ports/quake/sound/cdtracks also
Did you have to do anything else for that to work?
Edit: I've got this working now, I have .ogg files and .MP3 files in home/pi/RetroPie/roms/ports/quake/id1/sound/cdtracks and they are picked up in Darkplaces.
I've also got lr-tyrquake working, the same files in home/pi/RetroPie/roms/ports/quake/id1/music
I don't know if the original .ogg files I had were bad, or if having the .MP3s in there makes a difference, but it is working whatever the problem was.