Emulators are emulating N64hardware running a game pak, this is a native port of the game to Linux and unlocks several benefits. Off the top of my head:
Improved performance due to running natively on the hardware (not emulating an N64 with 4MB RAM)
Ability to set custom resolutions (widescreen), apply aliasing, filtering or other graphical tweaks
Easier to replace textures, models, audio files and otherwise tweak the codebase
Emulators are emulating N64hardware running a game pak, this is a native port of the game to Linux and unlocks several benefits. Off the top of my head: