I have spent a bit of time updating the wiki recently, I mainly worked on the sequencer and main user guides. You have highlighted that the webconf guide deserves some attention. Some of the settings pages have changed so there will be out of date images. Most these options are part of the midi protocol though, so they apply to many midi situations outside of Zynthian
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Program Change ZS3 (Program Change for SubSnapShots)
I believe this is about using your midi controller to quickly change between chosen patches on a single sound engine. There is a thread about it here that could probably be summarised and included in the wiki: ZS3 Programchange
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Bank Change with CC#0(MSB) & CC#32(LSB)
This is about changing the patch (preset) of the sound engine you have loaded, not all midi controllers have the capability to send these messages.
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Enable System Messages (Transport)
This option will show transport messages (e.g. start and stop) in the midi log page.
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Autodetect CC relative mode
There is an explanation here: How do I map a continuous controller in relative mode? - General discussion about Gig Performer - Gig Performer Community
Absolute mode is when the rotary encoder has been set up to emulate a pot or a fader (remembering the value of the CC being sent). Relative mode is when it sends a signed value to indicate moving up or down (and magnitude can vary based on speed).
The advantage of relative mode is that the up / down is always relative to the state in the software rather than storing (and sending) values as absolutes from the hardware. This avoids the whole glitch that can happen when you adjust a dial after a rack panel change (and the software syncs to the hardware).
This needs more explanation from one of the developers I think, not sure how it applies in Zynthian. I’m used to the midi pickup mode, not sure if they are the same thing.
Edit: more midi info here straight from the source - About MIDI-Part 3:MIDI Messages -