I don't think it is crazy, there are just some compromises one has to make. It is pretty hard to design a product that does everything, that is not cumbersome to work with. I might suggest a true bypass footswitch to take them all out of the loop.
For one thing, unless I am missing something, the bypass toggle using midi is a switch, once your pedals are out of synch (some on, some off), you will be turning some on and some off when you switch them all with the midi solution.
