There’s also inevitably going to be timing/performance-related bugs - the N64’s devkit docs say it runs games under a thin OS for multi-threading[1] so that’s another opportunity for things to go wrong.
Also, after conversion these games are still designed and hardcoded for an N64 controller and 4:3 aspect-ratio - that’s hardly “native” as far as PC gamers are concerned.
[1] https://ultra64.ca/files/documentation/online-manuals/man/pr...