I don't have my Axe in front of me, but I recall this was sorta solvable by pointing the FC pedal to an external controller. Then bind the external controller to the Wah instead. From what I recall, it still doesn't take the initial/value set properly when nothing is attached but you can easily flip the External 2 setting to None(?) in the IO and your WAH will function properly.
Above is from memory, hopefully I was close.