The explanation for TheFactor's "problem" is much simpler and more innocuous. The method used to set sub level in the "pre Audyssey" check is NOT the same as that used to calculate the trims during the "real" calibration. It's a much coarser method just to help you get in the ballpark of 75dB so the calibration program is guaranteed to not "run out of room" when it sets the sub trim.
Any idea why his sub trim is out of whack when it almost never happens to others? My initial sub set thingy always tells me to turn it down since I made a change - I ignore it and the trim is always ~3 db lower than it used to be. In other words, although course, it's accurate and consistent for me.
I still think he should set his sub higher and ignore the initial sub thing, which oddly, accommodates your explanation as well as mine (I'm 99% sure you're right, but I'd want to see some documentation.)