I have the exact same issue with the setup. I ended up keeping midi thru set for changing programs etc. Then used the aux switch inputs to control tap tempo. You can build a simple cable to come off one of the ground control loops, and go to several factor pedals. Then use that switch on the ground control to tap tempo and have all factors lock to that switch. If you are handy with a soldering iron it was pretty simple to find the combination to match your pedal settings that control tap tempo (such as tip or ring). Then have that combo in parallel and connected together going to the same single switch on the ground control. can't remember if the ground control setting is latch or momentary but that should be easy to see what works best.
YMMV- it all comes down to how you want to control your rig and adjust settings. For me, keeping tempo out of the midi world has worked the best. I am not syncing to any type of external sequencer or sync tracks, so if you need to do that then you'll need to keep tempo control in the midi world.
Hope this helps
Sean
