The game released at a very particular era where not only were a lot of us still getting accustomed to 3D, but a lot of us were still young to the point that we lacked a proper frame of reference for a lot of the things it tried to pull. Certainly there's some uncanny vibes in getting around that, and even the lack of understanding what was a bit of a rabbit hole for its time. I absolutely loved the game as a kid and it's still an all time favorite, played it for hours every day, but for sure it occasionally had an ambiance brought upon by an onslaught of unknown variables I just straight up didn't really understand at the time. The horrifying eel was one of them, randomly going downstairs to find a rabbit skipping in the pond was another, then running up the basement stairway to see a ghost spawn out of nowhere only piled onto things. Oh and just the uncomfortable feeling of being gobbled up whole by a fish creature in Tiny Huge Island. I'm sure I'm missing some other stuff. Then there was some more abstract stuff like the aforementioned lack of NPCs, Toads fading in and out of the world, and certain lines of dialogue. I played this game not being very adept at English for the time, so a lot of passages of text that weren't even really "hints" had me just confused and unnerved, such as being asked to walk quietly in the hallway or not becoming Nessie's lunch. Lines like those just had me on high alert not wanting to do something that'd come to get me.
My favorite story I've brought up here a lot is how as a kid I never understood what the deal with those butterflies were. Evidently a lot of people on these boards don't even realize that if you punch a butterfly, it has the chance of spawning either a 1-up or a heat seeking bomb. Because of the game's weird collision detection, it wasn't entirely uncommon for some butterflies to kind of detonate themselves. For whatever reason this used to happen a lot to me in my later childhood phases of playing the game, and they spawned those bombs so commonly that after a point I actually thought the game was out to get me. Stuff like that is why I feel like the Mario 64 creepypasta stuff about personalized cartridges and specific mysterious elements of the game kind of chips away at some kind of repressed faux-trauma from my childhood. Though I'm still adult enough to find it all absolutely funny and fascinating.