No, unless if you manage to program the midi controller to react to the start and stop signals sent by BB
Only the Main pedal on BB has Midi equivalent, the external footswitches 1 and 2 don’t have Midi equivalent. If they did then you could replace them with midi
But depending on the midi controller you might be able to have multiple functions per button, but one of the three buttons should be used to transition between these different functions
Personally I use both external footswitch and midi controller with expression pedal (MIDI Maestro) Originally I thought that I don’t need the external footswitch as MM has six buttons, but I was quickly proven wrong