It doesn't seem to work. Poring through the manual gave me no clue. Activating the tuner didn't mute it. Rocking the Volume pedal back eliminated any sound but I'm not sure that's how I want to go about changing basses. I run the XT Pro into a Peavey IPR 3000 DSP power amp which feeds each cabinet separately.
when you activate the tuner... there should be an option to mute the tuner... if you enable this, then it should do what you want.
assuming its like the pod xt. (non-bass version)