Here is the description from the manual :-
"Byp Vol - sets the Bypass Volume, the volume that this tone will be set to when the Amp+Cab block is off. It doesn’t affect the volume you hear with the Amp+Cab block on."
If you are always using modelling, then it will have no effect. It will have an effect if you are going in to the front of an amp without the AMP block enabled for example.