I have only played UQM, so I never realized how different the 3do and computer versions of star control 2 were. I knew the there were no voices, but in these videos the some of the music, a few game mechanics, some major graphical changes (planet landing... WHOA! how did you live??) and that planet lander bug were all different than UQM, and I don't think there was a planet lander bug in UQM. Something about the hyperspace music I liked better though.
You know, all you have to do is remove the remix packs and the 3DO music pack from UQM (or just never have downloaded them to begin with) for the game to run that PC version music. Especially big difference when you go into quasi space. Also, there are a number of graphical settings you can make in the latest build of UQM (0.5) that will have it use the PC version's visual content and methods. Just take a look around the options menu.
You know, all you have to do is remove the remix packs and the 3DO music pack from UQM (or just never have downloaded them to begin with) for the game to run that PC version music.
You don't even have to do that much; isn't there a command line toggle to use the PC music?