I'm a bit confused with your above as it seems to be more about becoming bass heavy vs flat.
I get the bass head part but I get all funny when it comes to flat vs bumping the lower frequencies and on top of that, running hot.
My question is to understand the why of it being done (philosophy) as opposed to the technical of what's going on. The quiz of my question is, we work hard to get a flat frequency curve and then we're encouraged to turn up the left third of the LFE channel while bumping the gain a few more dB......... huh?
After I run Audyssey, I use PGM2 and the result is flat bass. While I do get the 2 to 3 db increase from 40hz down with PGM2, it brings the overall response back to flat. For reasons I can not explain, my bass is "flatter" (south of 40hz) before I run Audyssey but Audyssey eliminates the bass ringing so the overall sound is much improved. By using PGM2, I end up with flat bass and have no ringing.
DEQ takes into account the apparent loss of low frequencies at volumes below reference and boosts it --- but I don't like the way it sounds. So, since I seldom listen at reference, I add a few db's to the bass for my own fixed version of DEQ. It adds a bit more "oomph" for action movies but isn't so extreme that it messes up non-action movies, or more importantly, dialog. I have seen graphs of Craig's response with PGM2 and that is how mine looks doing what I have described.