The MIDI channel used for on-board pi-Stomp hardware (footswitches, tweak knobs, expression pedal, etc.) is set in the default_config.yml file. Unchanged, that channel is 14.
External controllers connected via USB or a serial MIDI add-on, can use whatever MIDI channel you wish. How it reacts to those messages is determined by the MOD software. As you've probably discovered, midi learn listens for CC messages from any MIDI device on any channel.
There's been talk of having PC (Program Change) messages used for pedalboard control, but I don't believe that's been implemented by the MOD team and I'm fairly certain they've not built in any MIDI support for Banks either. That said, we could always roll our own, ie. create a midi listening daemon that calls the MOD API's (lame and lacking as they are) to do things like that.