Ok, so let me see if I have this right. First I need to save the pedal preset list to the phone. Then, in the phone preset list, I can copy really any preset, set it to bypass, name it bypass, then use that to bypass the pedal as needed. And I only need one bypass preset to put the pedal into bypass from any other preset. Is this correct?

Yes.

And you better casually adjust other parameters as well. As I said, there is a bug (I fixed it today but it will be available to you in next app update) where the H9 Control won't save the preset if you don't change any knobs.