The “Master Channel” is a MIDI channel that may be used to control zynthian itself, rather than instruments within chains. To enable it you select a MIDI channel from the “Master MIDI channel” dropdown. Then, sending program change 04/05 on that Master MIDI channel will select the next/previous snapshot. Be aware that note-on messages sent on this channel will control the zynthian as defined in “Master Key Actions”, e.g. by default sending middle C (60) on this channel will show the main menu view.
This used to be enabled by default but it confused new users because there were only 15 MIDI channels available for normal use and sending on channel 16 (old default) would cause unexpected UI changes.