The phase likely will be set same but since that's just polarity, just check to see if flipping one from 0 to 180 helps or not. Don't know if volume/gain controls are equivalent between the two models, maybe test the subs for equal volume (spl meter app?) before running YPAO (and I'd aim at 75dB for setup).
ps I may be assuming too much about phase adjustability being limited to a polarity flip from 0 to 180 degrees, didn't check what is particularly available on these