There are four available input ports for switches on the allinone encoder boards ( the later versions) and these are as you say allocated to the s1-S4 keys in most implementations. You can also add the zynaptiks board Using Zynaptik module for encoders [SOLVED!]
to gain four more digital pins which can be configured as ins and outs along with analog in & out, but this is still up for definition,. IT’ adds on as another 12c port so short wires are probably the order of the day between the boards.
As to pedal boards there is my zynthian saga of long standing, admittedly a diferent meaning of pedal board but a lot of the observations might be relevant. A pedalboard zynthian .. .
Which has explored a lot of the aspects you are describing.
I’m keen to bring a control panel out at standing hand level as I’ve always hated scrabbling round on the floor adjusting pots and driving menus on devices like the Roland loop pedals and such like.
However I do think a touch screen on the pedal end is useful. I have looked at using 4 + 4 momentary switches on the top panel to allow patch selection. Certainly any encoders that go down at foot level should probably be ‘robust’ or be protected with converted handles or such like to provide protection, not so much from a badly aimed foot, but more from simple lugging it before and after gigs around point of view.
I have been surprised how much space was used up in my case, and I’d look to working out EXACTLY what you do and dont want in the box . Mine has suffered from heavy feature creep but that has been experience based. I use audio in/out via an audio injector card ( as source of constant issues at the moment) and connector mounting and the essential bypass & reset switches need to be factored in. The other area that swallows space is power supply connections. I’m not sure I would trust too many type c connectors on a stage, so if you want rugged encoders and switches you probably should look at ruggedised USB, ethernet & power if you think you need these. Access to these connectors is particularly essential during start up and if your pedal board has as many strip downs and rebuilds as mine has had you will be glad it’s easy to get to the ssd card for changes and such like.
THe PSU quality is a them that you will find a lot round here. The type C supplies (if legit) seem better than the older Pi3 days but it’s still the major source of issue. It’s not as much fun doing Power Supply stuff as audio but , a quick intermittent on the PSU will spell curtains for your pedalboard and a reboot could be 40 seconds…
Hopefully this strange mismash of thoughts is of some use. Apicture of the considered box would be interesting as it helps to advice with a little context, and I don’t need to mention I will be hanging around like a vulture at a watering hole to collect a 
Once this is all completed !