The why is pretty well established - the original left and right signals get copied around to the center and side surrounds (and rear surrounds for 7-Stereo), then each channel gets bass management applied. At that point, the two channels that would normally yield a sub signal end up being five or seven signals, and those signals are summed together for the sub. The result is the sub getting more emphasis.

A workaround is something that I don't have as obvious an answer for. Having either mains or surrounds set to large (like Lonster) would eliminate the problem, but unless you really have large speakers it'll put you at a disadvantage in other modes. I asked Scott about applying the two-channel sub offset to these modes, but he indicated that it was problematic from a programming standpoint.