I'm looking to find a way to extract the soundtrack of this game in the most high quality possible, as it's not included as a bonus by GOG.

Anybody have any idea how to go about this, or what version I would be best sourcing the music from?

IIRC in PC version the streams are merged. 3DO version (Director's Cut) is the best one in this case since streams can be separated easily and it also includes music from D: The Novel. You can also extract a few tracks from the PS1 version in higher quality from what I remember. I've successfully ripped music from the 3DO version in the past and can provide a few tips on which software you will need.

You will need:
-- a copy of D (Director's Cut recommended) for 3DO
-- OperaFS Decompiler
-- ZStream CHUNKS Reader v0.4 (older versions won't work)

Extract the CD contents using OperaFS Decomiler.
Inside each CD there is a big-ass file (D00.3DO or something). Use Audio Data Ripper inside ZStream CHUNKS Reader on them. Then use Audio Convertation tool (SDX2 to WAV) inside it to transform these files into something you can listen to. The sound files are 22050hz, Mono, Compress Ratio 2. If you hear garbled noise, then try Compress Ratio 1. You'll get a lot of WAV files with ingame music (with sounds and voices, though).

D: The Novel sounds are AIFF files located in the NOVEL folder on one of the CDs. Foobar can play them easily.

My memory is rusty since it's been a long time since I bothered with it, so ping me if you encounter any problems. Cheers!

EDIT:

(adding info on GOG version)

If you want to extract music from the GOG version in case you cant buy a 3DO version from someone, you can just install Audacity with FFmpeg plugins and use it to convert the AVI files inside the game. The sound quality is kinda worse than the 3DO version though.