The not-libretro version Version of mupen64-plus has its own config files for buttons and other stuff.
Please refer to: Home · RetroPie/RetroPie-Setup Wiki · GitHub
But put /opt/retrosmc before any paths you find on that website.
e.g.:
/opt/retrosmc/opt/retropie/configs/n64/mupen64plus.cfg
or
/opt/retrosmc/opt/retropie/configs/n64/InputAutoCfg.ini