2 Observations, regarding the All in One schematic:
The encoder pin assignments seem to have changed from earlier versions,
old SW: pin 4, all in one SW: pin 2
old A: pin 2, all in one A : pin 4
(had an initial setback mixing old & new docs. re-implementing the circuit in my own layout)
High level signal levels of the MCP23017 I/O Expander are 4.3V (VDD – 0.7 min) with a 5V supply shown in the schematic, the SDA, INTA, INTB outputs seems to exceed Pi safety limits some have published. Short term encoder testing seems OK running the chip at 3.3V.