If you mean one sub is -3dB at 20 Hz while the other is flat, Audyssey might or might not "see" differences in in-room performance as the lower 3 dB limit for the sub, meaning Audyssey might not try to equalize the frequency response identically at 20 Hz.
On the other hand, if you mean one sub has a 3 dB advantage in output at high levels versus the other, things are different. Audyssey does not run high SPL tests to assess the power/frequency limits of the sub system. so all it knows is the frequency response in room at the level the test signals play back. not knowing one sub runs out of steam at 20 Hz 3 dB before the other, Audyssey can't "correct" for that invisible (to it) difference.