You can already do that. You can assign whatever CC you want as a bypass controller. It's on page 48 of the manual:
You can actually have a CC assigned as a bypass controller along with one of the on-board options. The one thing with that, though, is a value of 0 will be off and 127 will be on. So that won't really work with a MIDI expression pedal like you're talking about.
What you can do is use the CC associated with EXP1 or EXP2 (CC#1 and CC#2, respectively) and have your expression pedal mimic one of those. So when you do that, the auto-engage feature will work just like it would if you have the expression pedal directly plugged into the Stomp. So just change the CC assignment on the MIDI Mongoose (I'm assuming this is what you actually have, not the MIDI Moose, as the MIDI Moose doesn't have an expression input) to CC#1, and that will let you control EXP1.