The software did not find your switches. What you see is just the software defining the switches of the complete build. You use HW-version PROTOTYPE-4, which conflicts with the pins of the Waveshare.
You could try to use hw version "PROTOTYPE-KEES", which has the right pin layout for the waveshare and the Hifiberry Dac+. Use the wiringmatrix as in the fifth post when hooking up the encoders and midi.
Afaik the three buttons on the display are used as mouse buttons for the touch screen and read via SPI and thus not usable for the Zyntian UI.
Edit: pins are indeed on the pins 12, 16 and 18, but I desoldered them