The article linked above does comment on how the music was handled for the most part in the entire prequel trilogy.
Just compare the original trilogy and the prequel's respective soundtracks. The OT's music is mostly complete from scoring to screen, while the prequel's music is hacked beyond belief. Most of this can be blamed on Lucas's insistence on 11th hour editing. Within the 'digital age,' some filmmakers feel it possible to edit all the way prior to the film's release. There's a deadline to keep, so a score needs to be crafted even if the final cut isn't there. If further edits are necessary, the score suffers as well, unless the director and composer are able to score during these last minute edits.
The OT was mostly finished when the original scoring was done. Sure, further edits were made, but the score wasn't butchered to accommodate them. Some tracks were looped, but major edits do not abound. The prequels suffered from massive edits after scoring was complete and we got what we got.
I don't know if anyone outside of Lucas and Williams will know what really occurred during the scoring and editing process, but I think Lucas may have gotten too involved with the music, just like he was too involved with every other aspect of the films. He over thought the minor things and was blind to the larger picture. Some directors can handle multiple mantles, but Lucas isn't one of them. He's a visionary and a great producer. He's not a writer, nor is he even an average director. The prequels in general could have been handled better if he delegated authority better and left the ego behind.
But I'm getting off track.
My gut feeling is that Lucas pulled Williams back one too many times during the scoring and Williams threw his hands up and relented to Lucas's ideas, good or bad. With a more balanced give and take relationship between the two, and a more finalized cut prior to scoring, the soundtrack and films in general could have been significantly better.Not to mention, Ben Burtt should not be editing film, nor should he continue to believe that sound effects trump an epic score. Like the article said, I remember sitting in on the first screening of TPM and yelling "turn it up!" during the opening fanfare. I though they'd get the mix right in the next film. Boy was I wrong.