Obviously this is just a personal judgment, but I believe N64 is currently understood at quite a good level. Most of the docs are on https://n64brew.dev/. Low level efforts are recent for sure, though I'm not sure I would rate them as "not mature". Ares is able to run most of the library (including 64DD) and all the homebrew library with zero per-game configurations or tweaks.
The one game I am aware of and keep checking is "Wonder Project J2 - Koruro no Mori no Jozet".
Broken in both Ares and the miSTer core. AIUI nobody knows why it does not work yet, which shows gaps in the understanding of the machine. Otherwise not an issue for me, as I can run it on the actual hardware, which I own.
Note that, in no small way, I do appreciate the efforts. The state of the art of N64 emulation is much better now than just a few years ago. But it sure is not there yet.
N64 also happens to be by far the heavier console to emulate in 5th-gen group. The unified memory architecture poses unique challenges for cycle accuracy, given that conflicting accesses by different peripherals are serialized in various ways, causing stalls, and also non deterministic behaviors as the signals cross different clock domains.
So the issue is in part that this level of detail hasn't been fully reverse engineered yet, but that's because there is no rush since the information wouldn't be usable anyway right now in an emulator.
I am hopeful as ModRetro's m64 launches, with a FPGA larger than the one in the miSTer, and there's an associated influx of developers looking at the platform, we'll see renewed energy directed towards understanding the N64.