That will likely require full decompilation. This is akin to wrapping the emulator up with the rom, with a few common functions (found via decompilation) being updated to support more modern rendering approaches. This isn't so much "native" as it is a patched container in an executable form.
EDIT -
But hey, you can always just add another layer of emulation via Proton to run it in Linux.
I don't think that's true, it really does recompile the N64 games into native executables, you can compile them using any C compiler like msvc, gcc and clang.
EDIT - But hey, you can always just add another layer of emulation via Proton to run it in Linux.