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...
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An arranger is just a tool. What matters is what you build with it..!