I wouldn't be in favor of the 'Factor pedals incorporating that kind of 'slash-and-burn' solution. As for an external device, I'd suggest my favorite go-to MIDI toolkit – one of the MIDI Solutions Event Processors.
I run a fairly complex MIDI routing, and I'm thinking aloud on how this could adversely affect it (assuming that I was changing algorithms in a mission-critical situation). Start / Stop? That's usually generated 'upstream". Active Sensing? Totally screws up an FCB-1010 pedalboard. Aftertouch, Pitch Bend, and CC messages? Most certainly. Note Offs? Could be problematic.
The other semi-innocuous messages? Maybe not so much. I guess what really bothers me is that – for as often as I have a MIDI monitor up – I've never noticed this before. Then again, my patch programming sessions are usually isolated from my recording or live situations.