One thing to note is that Nintendo doesn't really have any intrinsic advantage over the unofficial emulation community just because they produced the NES. Whatever documents they have archived internally (something along the lines of this: https://archive.org/details/famicomdocs ) would just document how the system is supposed to work and how well-behaved software should work, not any of the quirks and edge cases being tested for in the video. I think it makes sense that Nintendo didn't bother making an accurate NES emulator until they moved to the "emulator and a bunch of games" model with the NES Classic and Switch Online. The "emulator bundled with each game" model used by the Virtual Console allowed them to avoid doing all that difficult hardware analysis work. If a poorly behaved game exposed some inaccuracy in the Virtual Console emulator, they were able to add a hack to that game's build of the emulator to make the game run correctly instead of having to figure out what strange hardware behavior the game was depending on.

At this point I'd even say the community knows more about the differences between the various APU and PPU revisions than Nintendo themselves did.

Did you see the "Donkey Kong 25th Anniversary" NES hack that Nintendo did, that shipped on red Wiis in certain regions? It's one of the sloppiest hacks I've ever seen. Based on that alone, I'd say the community knows more about the NES than current Nintendo does.