Hi Adam,
There are a couple ways to bypass an Eventide Stompbox via MIDI. You can use MIDI Program Change or MIDI Continuous Controller. You may have to check the user guide of your MIDI controller to see if it can transmit both of these types of messages or just MIDI Program Change.
In the Eventide Stompbox's System Mode under MIDI there is a menu called RCV MAP. From here you can set what the stompbox will do when it receives a certain MIDI Program change number. The choices include loading any of the stompbox presets, Bypassing, going into Active, or Toggling between Bypass and Active.
For Continuous Controller there is a menu called RCV CTL. The first choice is Bypass (BYP) and you can select any MIDI Continuous Controller number to control Bypass.