To be more clear, there are 3 n64 cores total on batocera v31.
Mupen64plus (libretro) - can enable/disable fbe
Mupen64plus stand-alone - glidemk-2 - missing option to disable fbe, but is the only core that will run some of the n64 games at full speed, including 007. Many options in config txt for various things related to “frame buffer” but nothing specifically for frame buffer emulation.
Mupen64plus stand-alone - gliden64 - has the option to disable fbe in config txt
I tried messing around with some of the other frame buffer settings in the config txt for the glide-mk2 plugin, thinking that maybe it could be named something different, but none of the changes made any difference.