The only issue I can think of for using a volume pedal post-everything is, is the controller input pre-distortion, or at least, pre output stage distortion?
On a real Hammond, the grind winds up as you push the accelerator to the floor (

), but if you put a volume pedal after the main outputs, you are going to be simply ramping up and down the already distorted sound.
Not quite the same effect, IMO...