I tried that and that worked alright but I was disappointed as it meant I'd have to switch other things in and out dependent on patches even if I wanted to run them as 'on at all times' (I.e. noise gate).
I fiddled around more last night and solved the bypass issue. Setting the CNT1 and CNT2 midi controllers to send the right CC# (I set it to 04 on TimeFactor) value 00 and value 127 respectively got it so I can activate/bypass by stomping again on that patch key (setting 127/0, on the other hand, makes the patch inactive by default, great for my dry patches).
Now to figure out taptempo... God MIDI is a heck of a lot of work...