It’s a bit more involved than just a config file, but actually compiling it yourself.
This post was one user’s tutorial. (Ie just scrolling up)
There’s references to using the NEON instructions that are present in the gameshell, and possibly a contributing factor re: speed optimisation. This is also something you should do when updating cores in retroarch, and mentioned in this thread. (Nothing to do with mupen64, but for the sake of context re NEON)