This is more of a work flow issue for studio use. If in Stomp Mode and all my stomps are utilized, there is no way that I see to engage or disengage any additional modules without temporarily setting them to one of the stomps, engaging/disengaging it, and setting the stomp to the original module.
A simple bypass button on the modules controls, similar to what is there in Scene Mode would be useful and simple. This would make “auditioning” sounds so much easier.