Interesting! I listen to so little HT that I have never thought to compare it with the surrounds engaged!
That is really strange that it would emphasize the surrounds. Sounds like a design glitch.
In theory, at reference levels it should do absolutely nothing to color your sound, assuming you have no "reference level offset" assigned...at least that is my understanding!
I also run the Audyssey flat curve.
From the Audyssey website
Audyssey Dynamic EQ™ adjusts the frequency response and surround volume levels moment-by-moment.
Part of the dynamic EQ design is to boost the surrounds. This is to make it seem like you're getting the same amount of material from the soundtrack delivered to you, just at a lower volume. IMO the result is mediocre at best, unlistenable at worst. I love movie soundtracks and scores, effects included, and to my ears dynamic EQ falls well short of the actual soundtrack at reference level. The whole point of reference level is so that you hear what the sound engineer heard and wanted you to hear and with that proper balance. I think dynamic EQ too often throws that balance way out of whack.
I may be misquoting Dr. Mark, but IIRC he said that the Audyssey flat curve does not accurately reflect real world sound and while he is no fan of the Audyssey curve per se, it more closely resembles how things should sound. Again, IIRC the Audyssey curve tapers the high frequency response down a bit, which is supposed to happen with high frequencies as distance from the source of the sound increases. Audyssey flat keeps the FR flat at your seat, which creates an imbalance and slightly unnatural sound.
Now the Audyssey curve may also do other stuff that he may not like, but from my own measurements it has never created any other unnecessary bumps or dips to the FR other than the slight taper of the high end. I think my hearing tops out in the 18,000 range and I couldn't say definitively that I hear a significant difference between Audyssey and no Audyssey for the majority of material after proper placement and all the stuff I go through to get the bass the way I want it. Now between Audyssey and Audyssey flat, I
think I hear more of a difference and it steers me towards the Audyssey curve. For instance, I
think the ripping paper on the Linkwitz CD sounds more natural with the normal Audyssey curve rather than the flat. As does the train whistle and some of the other real world examples.