no, no current or previous version of MCACC has a dedicated EQ just for the subwoofer channel.
but you are correct, 63 Hz is the lowest freq for EQ'ing bass from speakers set to Large. for speakers set to Small, the lowest will be 125 Hz.
the standing wave filter, however, does do 3 notch filters on combined bass, freq's & width of the notch will be automatically set by the receiver or you can manually set them, providing you know what the Q value is for
and phase control maintains phase integrity on bass from subs and speakers and speaker drivers themselves. Pioneer puts a lot of emphasis on maintaining same phase as part of audio quality.