One advantage that GoG has over Steam and the other platforms is that most games come with a downloadable soundtrack that you can listen outside the game. But where does it come from? For example System Shock 1 has the music in .midi .mp3 and .flac. How did they get access to a flac version of a 20-year-old game's music?

Presumably they got them from the owners of the soundtrack or from the people who have distribution rights.

So far as getting a flac version of an old soundtrack that just comes down to what source they had available. They could have studio quality recordings on tape or a some other high quality source. Music has been being recorded in high quality formats for a long time before digital options were readily available. Making it available in a high quality digital format is pretty easy if you have a high quality source.

It’s.......magic!!

In this particular case, a lot of it is (or was, I haven't checked recently) fairly unsatisfactory.

The .mid are probably put together from data ripped from the game. It's not a straight-forward conversion since the music changes dynamically when there's combat and such, so the composition used here may be arbitary. They seem to play at the wrong speed too. Probably put together by a third party, not gog.

Quite likely the .flac have been made by putting the .mid through a crappy midi player and the .mp3 by putting the .flac through mp3 compression. Both of these are rather useless.

As far as other games are concerned, some used to have their music as audio tracks on the CD or a few even had a soundtrack CD released, both of those are great sources for a .flac. If such is not available, the original producers may still have higher quality recordings around. And failing all that you can still rip the music from the game or just record it as it plays.

Likely original CD-Audio discs (for the games these were released, at least), or maybe from high-quality rips from the "scene"...