I wasn't able to map the hotkeys on the keyboard which is configured as a controller, but since I will use pyAutoGUI and scripting for GPIO inputs, I that's not a big deal.
The keycodes found in mupen64plus.cfg relate to ascii characters, and so I remapped the functions I plan to access later via GPIO to keys I won't need.
Here is simple overview I used to figure out key-values: Ascii Table
You have to look for the decimal values.