I agree on this not being a case of "bad code", but it also clearly isn't the hardwares fault. There's tons of other platformers on the N64 that run better, look better and have less glitches. The comparison is obviously unfair, but there's so much more you can do with the hardware with modern optimizations it's insane.

The actual reason the game is so buggy and broken in so many weird places is simply because it was their first 3d game and it was made by like twenty people in barely three years. The tools they must have had to make the game must have been ridiculously primitive. It's frankly insane that it actually turned out good. There's never going to be another guy like Miyamoto.