To switch the TF into Bypass via MIDI I do the following.
On the TF go into the MIDI Menu then go to RCV CTL and there set the value like this:
BYP < C20 (C20 means CC20) CC stands for MIDI continuous
On my MIDI Footcontroler when I send a CC20 to the TF the TF goes into Bypass.
Works great for me. Of course you can use every CCnumber you like. 20 was just a sample.