Right, I agree. So when Audyssey does the "your sub is too high/low" level thing, just ignore it and lower the sub?
I would say so, based on my experience with both my Marantz AV8801 and Denon AVR-X4400H, but that's not the case with my AVR-X1800H so I guess it depends on the model. Regardless, afaic, D+M messed up the red/green (or what you might call high/low) thing. In many cases one has to ignore the red (too high) warning, and lower the sub level until the bar hit a little over the mid point, that is, into the red zone by about 1/4 way.
That should land you level trim set to about -3 to -7 after calibration, then if you want a tilted (up) bass in the deep bass range, you should adjust/customize the target curve, or if you wan to b e lazy, just adjust the sub level trim up by about 3 dB and call it a day. Customize the target curve is, obviously, a preferred way.