When comparing 2 subwoofers and 1 sub has 3 db advantage at 20 hz over one sub, will Audyssey correct this to make the advantage of the other sub mute ?
The term "Flat Frequency Response" is actually +/-3dB, however, die-hard subwoofer fans don't settle for anything less than a ripple-free ruler flat response.
Audyssey may or may not make up for -3dB at 20Hz. It depends on what the flatness target is encoded in Audyssey. But if it does fill up -3dB, it will be actually cutting the sub amp power by half. You may get away with 3dB boost at 20Hz if you are running something like JTR OS with amplification power in spades, but your sub will surely will run out of steam if it has average wattage figures.
I reckon if you are in +/-3dB ballpark, consider yourself lucky. Audyssey or no Audyssey