Is there any way to have the Pitchfactor behave as if the expression pedal is plugged directly into it? Thanks!

You may connect your PitchFactor to your PC/Mac through a USB cable. In H9 Control, you may adjust your presets and all the settings of your PitchFactor. 

You may map the expression (Hotknob) and all parameters to certain MIDI CC messages. To do so, please find the attached screenshots (1->2->3->4).