I suppose by writing clever self-modifying "ROM" code, you could hack the Pi into acting as a coprocessor, but in this configuration, it's just feeding arbitrary game data to the N64 - emulating the ROM that would be seen in a normal N64 flash cart.
Unlike in older consoles like the SNES where cartridges often contained processors and other logic, N64 flash cartridges were by and large just ROM, save data EEPROM or SRAM, and a serial bus for simple peripherals like an RTC or modem that I think was only used in a few very rare games.
The particularly interesting thing about N64 flash cartridges is that they have a seed/key/checksum security mechanism implemented using a chip called CIC. There's a good video about it here : https://av.tib.eu/media/32818 .