Yes that would be another current disadvantage; presently you can only call up a preset as "Active" via MIDI. This is something that other users have pointed out and we are addressing this in the next software update. 

A current workaround would be as you mentioned,  to save a preset as "dry, " ie with all knobs fully counter-clockwise (on ModFactor use the Tremelo Effect.)  

Another thing to consider is that you can use one aux switch with a "Y" adapter to bypass both stompboxes at once.