For those that care: Wilson commented on this around the time of the Misplaced Childhood release (you can find the interview via Google). To do a 5.1 mix, he HAS to do a new stereo mix. For some, it's a radically different mix than what we previously released, in other cases it's not that different at all (and in the case of MC, it was almost exactly the same). I don't think he named names, but it was sort of evident (as I remember it) that with Crimson, he gave the stereo mixes to Fripp, who released them because he's a completist, and released everything. With Yes, he seemed to point the finger at the record company, who tacked on the stereo mix as a marketing gimmick, even though it wasn't that different than what came before. He explicitly said that he wasn't contractually obligated to give the new stereo mix for MC to the band, and he felt that his work didn't improve on what Chris Kimsey did before, so he withheld it. Apparently he didn't feel so charitable toward the original Brave mix (my CD doesn't say explicitly but it seems that Dave Meegan did the original mix).
As an aside, I don't know if there was a bridge burned or not, but it seems the band is distancing themselves from Meegan (and using Michael Hunter, who was an engineering assistant under Meegan). It's a shame, because the work with Meegan is my favorite of the Hogarth era: Brave, Afraid of Sunlight, Anoraknophobia, and Marbles.