It’s not an os problem.
Encoder/GPIO Works with stable. I have two machines running this way.
Zynthian-amp.local A hifiberry 60W Amp Pi3 combi …
as detailed here.
The other is zynthian-alm.local which is audio injector card based machine. IT’s wired slightly differently, ( one pin is on a different i/o pin. )
It’s really down to the internal layout of your encoder and Pi combination. That’s how I chose the pins to minimize the crossing over and general wiring mess. With stable avoid the SPI allocated pins.
It’s perfectly possible to run just encoders or switches by appropriate settings in webconf. IT makes for a good test to just see the response from the switches because a miswire produces a very confused encoder response as the button gets pressed by an encoder twist by mistake.