What I am trying to convey is that Audyssey MultEQ Pro (the software) can be told (by the installer) that a Sub Equalizer is in the mix (isn't something very similar already done in the SubEQ software for the SVS AS-EQ1 to tell it that MultEQ is in the mix?). Therefore, no matter what information the AVR passes back to Audyssey MultEQ Pro for each sub boink (produced by the AVR), Audyssey MultEQ Pro could ignore those values and use perfect/flat/whatever values in their place when calculating the sub filter that Audyssey MultEQ Pro uploads to the AVR in the end. The AVR doesn't need to know about any of this, just Audyssey MultEQ Pro (the software on the PC). What the AVR doesn't know, doesn't hurt it.
Furthermore, since the AVR waits for the installer to move the Pro mic to the next position (position 2), here is a good time to have the Sub Equalizer connected to the PC as well. Here, Audyssey MultEQ Pro could tell the Sub Equalizer to do its boink(s) using the exact same mic position. Then after those measurements are collected and transferred from the Sub Equalizer to Audyssey MultEQ Pro, the installer would then be told to move the Pro mic to the next position. This whole time, the AVR is still thinking the installer is moving the Pro mic to the next position (position 2).
For this to work, the Pro mic would either...
1) have to be connected to the Sub Equalizer and passed thru to the AVR. Audyssey Pro would have to tell the Sub Equalizer which boinks to pass thru for the AVR and which to keep for it's use. Each piece of hardware would be responsible for passing what they "heard" back to Audyssey MultEQ Pro (either by serial or USB cable).
2) have to be connected and dis-connected between each piece of hardware between mic positions if there is not a pass thru option on the back of the unit (somewhat similar to the SVS AS-EQ1).
Here I go again over simplifying things and mucking up the thread