Not ignoring it at all, just pointing out that it makes no sense, since the second round of equalization changes the settings that originally made the response of each sub flat, thereby rendering the first round of equalization pointless.

Whether you want them to not, the two subwoofers will interact with each other. Rather than take my word for it, anyone reading this thread can try it at home. Equalize two subs so that each one is flat at the listening position. Without moving the measuring mic, turn on both subwoofers. Notice that the response from two flat subs now looks like a roller coaster, because their interaction wasn't taken into consideration. I suppose you could then do a second round of equalization, but now you've just changed the original EQ settings to what they should have been from the begining.

A better, simpler, easier and cleaner approach would be to measure the interaction between the two subs, since that's what you're going to hear anyway. IF it is possible, move one or both subs around to see if you can improve the frequency response, in which case you'll minimize the amount of correction that the EQ has to do (always a good thing). The box was designed and built by Audyssey. They allowed the option of EQing each subwoofer independently because the box can take in a stereo input signal. Two separate signals require two separate equalizations, since their interaction can change based on content. At the time, Audyssey used to EQ each subwoofer channel independently, like the 3 subwoofer outputs on the Denon AVP1 (again, because each output could carry a different signal). They have since wisened up and now send the same mono signal to each AND globally equalize their interaction.