I got round this problem by simply turning the Stomp volume knob right up and adjusting the input gain in the preamp to avoid any clipping etc.
I found the noise from the pc was there at all volumes in the stomp. The signal quality in no way was dimished by setting the Stomp volume to 100%.
The only worry/danger is that you can't use the headphone output directly but I use the headphones out put on the preamp so this wasn't an issues with my set-up
I tried the volume control in the effects block set up with a pedal controller: worked well - absolutely no noise noticed but a little awkward to set up each time.
The opposite is true for some tube effects I've got where increasng the o/p also increases the noise floor.