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I've not used a port expander personally but they seem pretty simple wiring wise, so they should be fine. You don't have to go through SimHub with a button box, the classic AMStudio sketch https://github.com/AM-STUDIO/32-FUNCTION-BUTTON-BOX works fine too (on a leonardo or pro micro).
Yeah SimHub has a great tool for making it with no code writing, but if you want to add port expanders and things, you'll have to code it yourself. https://github.com/joeyoung/arduino_keypads is a library that will allow you to make a button matrix with the buttons connected to the port expander. The rotary encoders can go direct to arduino pins.