@adamg thanks for sharing this. I just updated to Buster and my old fix for mapping the generic n64 didn't work. Mapping a hotkey for the menu did the trick. Weird though, I only had to map my A and Z buttons, everything worked fine.

The input configuration for Mupen64Plus is kept separate - this is documented at https://retropie.org.uk/docs/Nintendo-64/. Look for the sample configurations, there is one even for the N64 usb controller.