Hi, I have a weird solution to this.
I have an MPK Mini acting as my second control surface to act with my FaderPort V.2.
I noticed something I can do, while midi mapping my MPK like a savage on Logic.. on the "No Zone" I was mapping my MPK on, I tried mapping the FaderPorts bypass button to bypass the first plugin on a selected channel. That works, however I haven't tried mapping by pass all button to bypass all in logic, I think logic only gives you the option to bypass all plugins in a session not on a track but I could be wrong.
Point is, if you do this you'll be able to do something with the bypass on the Faderport that bypasses stuff. I hope this helps somewhat.