Both the M13 and Piranha have MIDI, right? You should be able to have the M13 switch the Piranha when you switch scenes on the M13.
Now, if you mean that you can't get the M13 to switch MIDI devices when you switch individual effects on and off on the M13, then yes, that's a limitation of the M13's MIDI implementation. If that's the problem you're running into, the only solution I know of is to use a separate MIDI foot controller to control the M13, Piranha (and Y-Not). A sufficiently advanced one would be able to switch presets on the Piranha, scenes and pedals on the M13, and presets on the Y-Not.