very unlikely the audyssey mic is significantly "off" in the bass. Depending on the setting you use the Radio Shack meter intentionally either rolls off a fair amount (C weighting) or dang near all (A weighting) the bass so it's a litttle hard to trust . . .
If you don't listen hugely loud, then bass will appear shy because of the equal loudness curves (google 'em). Audyssey's fix for that is Dynamic EQ which at least in theory can provide better "'correction" than simply turning up the sub. But see the Audyssey thread for good info on the "tricks" to use DEQ with music, and the reasons we have to use those tricks). The setup guide and the FAQ are linkesd all over the thread and are chock full of valuable info distilled from the input of Audyssey's own CTO as well as the blood sweat and gratuitous cursing of many members (well, at least me) as they learned to use the system to its best.
And, FTR, a goodly number of folks around here run their subs on the hot side. None has been condemned to any torture or undue heat (although those in the NE might like a little undue heat right about now).