It’s not a “real problem”. It could be done, but current code doesn’t allow it because until now nobody tried this combination. That’s all 
Currently you can use these configurations:
- 1 or 2 x MCP23017 (interrupts)
- RBPi GPIO for switches & encoders (interrupts) + MCP23008 for switches (polling)
I must apologize because the zyncoder.c code is a mess. It was one of the first pieces of zynthian and it needs a deep refactorization, but as it works quite well and it’s highly critical, i’ve no incentive for prioritizing the task. Mr @riban is pushing to me for doing the task, so perhaps you could joint your forces and increase the pushing … or do the task!!! 
Regards,