Its weird, because Episode I has a pretty good sound mix, and Young Indy always had pretty good accolades. Of course its been a long time since I saw Episode I, and longer with Young Indy.
The low music levels definitely trace to Burtt, either because he trained Wood or because he was supervising. Theres a really interesting moment in the Episode III DVD doc, where they are sound mixing. Burtt has the music turned down low and the sound mixer, an older experienced guy, chews him out and says theres no point in having music if its that low. Its the only moment I've ever seen in the prequel footage where a guy stands up to Lucas and says, this is crap. And in the end, he makes Burtt turn the music back up so its louder than the sound effects, and Burtt sort of slinks back in his chair.