I'm not really sure why. When you look at the diagrams, the controllers still use a wire for each position. For example, the main air unit has a stepper motor that switches between floor, split, and upper vent modes. Seems like you "could" take an arduino relay board and a small touch sceen and bypass all of it. Lots of splicing unless you can get connectors or pull pins and replace.
Sounds like you know how to deal with it. Please prototype and share your results. Thanks!