Just to close this off, I finally got round to having a listen to the Queen DVD again after re running Audyssey. While it seems a bit better than previously, I think I just prefer this disc with Audyssey switched OFF: It just seems to add an edge to the sound that I don't like, though it could be due to this being an older disc and only DTS rather than DTS MA.
What it does mean is that I will try to further improve my manual Pre Audyssey subwoofer/crossover results when I can measure with only one speaker at a time, so I'll be able to have a good bass response without using Audyssey, but without the 'edge' added to music. I think I still like using Audyssey for surround (movie) content because it helps to blend the speakers together and at least when I drop my screen it dampens the higher end a little (not unlike Re-EQ) so perhaps I should just do my Audyssey set up with the screen up and then lower it to act as a treble cut.
It's worth remembering that Audyssey was never designed to work with music really. Music has no standardised content criteria so it's all a bit of a kludge. Various combinations of DEQ on and off, with various RLOs have all been tried, with varying degrees of success for music. Quite a few members report preferring Audyssey off altogether for music and use it only for movies. I can’t comment as I don't listen to music as such in my HT room, favouring a separate, ancient, 2-ch system in another room for music.