I’ve just looked into this in the latest MODEP version, and it looks like it is somewhat possible to do, but works in the most unobvious way imaginable.
First, you have to edit /var/modep/profile5.json and set midiChannelForPedalboardsNavigation to a chosen channel between 1-16, and same for midiChannelForSnapshotsNavigation if you want to be able to switch between snapshots too. It would make sense to use different channels. Any number outside of [1;16] range means disabled.
Changing snapshots works just fine.
Here comes the amazing part - changing pedalboards works, as long as there’s no open web sessions. I have no idea why MOD designed it this way.
Other than this, you could look into MIDI Command Server - you could make your controller trigger shell scripts and do whatever you want. 