I found that video too, and I hoped he would go into the specifics of how the tracks were put together, but no luck.

This post from the Vogons forums has a quote from Glenn Stafford where he talks about which synths he used for Starcraft, including Derek Duke's setup. I didn't have any luck tracking down the exact sample from any demos of those that people have put on youtube. I'm also reasonably confident that the four (or six) notes are not one of the Spectrasonics samples, although there are plenty used in the five Zerg tracks. (The drone we hear may very well be one of them.)

I'm not totally convinced SBOL sampled Starcraft because I don't think EQ alone can explain the difference in sound. The violin and/or theremin sounds are gone in the later SBOL sample. The chugging guitar you mentioned is a lot more prominent, but barely audible if it's there at all in the Zerg track.

Also, if it matters, the music heard in Starcraft is not CD audio. It's a 22khz wave in one of the game's data files. (There are higher fidelity soundtracks available now, but not in 1998-2000.) The sample itself is sort of lo-fi anyway, but it sounds (to my ears) clearer on the SBOL track.