I got the game on Steam through the semi-recent humble bundle, and managed to mod and edit it into working at 1680 x 1050 with hardware acceleration. I was wondering if GoG has made any significant changes outside of making the game able to run out of the box, so to speak.

CD music

Probably not; GOG simply focuses on getting the game running like it ran "back in the day". Sounds like your version is just as good or better.

A.The CD music, which is not in the Steam version
B. It's runs much more stable and you have less problems with the graphcis then you did with the Steam Version.
It's not so much that, except for the music, GOG added anything,they just did a much better job of tuning JK to run smmothly on a modern computer.
IMHO those two things alone make it far superior to the Steam release.

None of the steam versions run by the way

They do. Sounds more like system specific problem.