This game has a very unique soundtrack that, sadly, was compressed down significantly in the original release. Did GoG manage to get their hands on a version of the OST that doesn't sound garbled?

In-game music sounds better than this version, which has been ecstracted from the original:

[a link should be here, but it doesn't work. Google "Chaos Gate OST #005 - Ultramarines Chant | Warhammer 40K Soundtrack Music"]

You even get the full OST in MP3 version with purchase, so I strongly believe it has been repolished for GOG release

All copies of the soundtrack floating around the net were originally ripped from the game data.

Most of those have been downsampled and all are guilty of being transcoded to a lossy format from a lossy source (the in-game music uses ADPCM compression), sometimes multiple times over. Downsampling degrades sound quality.
Each re-encoding to a lossy format degrades sound quality, and after multiple transcodes, the result sounds like - not to put a too fine point on it - garbage. This includes copies you can find on YouTube (WAV -> MP3 (lossy) - > to video (lossy) -> resampled by YouTube (lossy)).

What I see in GOG's version matches what I remember about the tracks from an original disc release. MP3 format does not say anything about its source or quality - anyone can chuck the WAVE files from the game data (check the WAV subdirectory in the game directory) into something like Foobar2000 and convert them to MP3, FLAC or any other format that suits their fancy.
Judging by the sampling rate and bitrate, the soundtrack has been converted from the original files, which means it WILL sound worse (lossy-to-lossy conversion as mentioned above).
Some years back (okay, closer to a decade now) a group of modders tried to reach the owners of the rights to the game to use the music in a Dawn of War mod. If my memory serves, the rights owner apparently lost them, and so did the original composer (in fact, it is so bad that the actual track names are lost).
Unless you get an actual announcement from GOG that they have obtained access to the original master recordings, it's unwise to assume they did.

Thanks for the replies. It's good to hear that this version sounds a bit better than the weird abandonware version at least. I've attached an image of Audacity having both the music from the autorun program and music_combat4.wav from the abandonware version open (same track). I amplified the autorun track a bit but didn't change anything else. The audio from the actual game looks like someone screwed around with it to me (loudness & clipping?), but I'm by no means an expert. Bit odd that they decided to do stereo sound but 22050Hz only.

That's not what I said. What I said was that the numerous bootleg "soundtracks" sound worse, because they are ripped from the game data. Not same track, check in the \Wav subdirectory of the game directory. Not in the context of when it was released (mid 90's) and the hardware it was supposed to run on (166 mHz Pentium, 16 MB RAM). Game developers had to run a very careful balancing act between asset quality, size and performance of their games.

If they had space on the CD, they'd probably store the music as audio tracks on the disc (cf: Heroes of Might & Magic 2, Cyberstorm 2, Incubation). However, that would reduce the amount of space available for the game itself - and when the other assets accounted for over 600 MB (with a CD only taking around 700 MB), the audio had to be compressed to save on space.

Downsampling it reduced the performance impact caused by decoding the audio, cut back on the data transfers (important given the faily low transfer rates of the HDDs of the time) and saved space. On most of the soundcards/speakers/headphones in use at the time, the practical difference would have been minimal.