Can the assignable Touchpads or Controller Knob be linked to MIDI functions?

No, The A B C assignable Touchpads are only assignable to the functions listed in drop down menus within Apogee Maestro 2's Device Settings Tab or in Apogee Control 2's System Settings sidebar.  Each of the three Touchpads can be configured to Dim the output level, Sum to mono, Mute, Clear Meters, Engage Speaker Sets, or none.   The controller knob can be only be set to Mute All, Speaker, or Headphones when pushed. Rotating the controller knob adjusts the level or gain of the selected input/output.  These can not be linked to any MIDI functions.