Looks like a makefile issue, as some neon asm is not being built/linked correctly. Older sources work.
Currently bisecting.
I was also trying to debug this, great you are taking care.
It's this commit https://github.com/libretro/mupen64plus-libretro/commit/e54a7279d5610602177c3fcaa6f747a7c0547cfd
The logic as it is now, platform gets "unix" added to it for RPI, and then the rpi logic later isn't included.
I have a fix which I will open a PR for.
PR opened upstream
Great job @joolswills, your PR got already merged upstream and I can confirm lr-mupen64plus is compiling fine again from source on my RPI3b+. Cheers.
thanks.