The canyons are a weird thing that's pretty unique to this game, now that you mention it. I feel like they're an intentional part of the world in some fashion too and not just an excuse to give the map an edge, because the game prominently features them in a variety of roles and contexts. You're constantly passing through canyons between more open areas, Kakariko Village is in a canyon, there are ways to get across the bottomless pits in spots like Gerudo Desert, etc.
Then there are the very extreme changes in elevation. Lake Hylia is this huge pit that isolates Gerudo Desert from the rest of the world and it's impossible to imagine how anyone is supposed to get in and out normally without using the bizarre clown cannon and chickens setup. Death Mountain is this twisted mess of torn up earth with random metal objects embedded in it with no clear purpose and this weird floating meteor in the background that was maybe supposed to represent the top of the mountain somehow. You have the high canyon walls of Kakariko, Snowpeak's valleys and chasms, Zora's Domain is very high up now with all these rivers and waterfalls... The whole world feels rocky and torn apart compared to other versions of Hyrule. It actually reminds me a little of ALBW's Lorule, now that I think about it! It has kind of a "ruined" vibe to it, like it's existed far too long and is falling apart in a lot of places. I don't know how intentional that was, but the early Hyrule Castle sequences give the impression of a monument that's impossibly huge and in a state of disrepair, it's in just as bad a shape as the crumbling ruins dotted throughout the rest of the world. Like the current royal family is just squatting there. Some parts of the world just feel incoherent and strange as places that actually exist, in a world that is on the whole not trying to be very fantastical. I think most of all there's just a severe lack of context and explanation.
For me the big upfront thing in Twilight Princess that it feels like the developers wanted you to ignore is the Twilight itself. The residents of Hyrule are mostly unaware of it and just seem very detached from the world in general. They have that whole thing with the resistance group, and you need to seek out those characters as part of the process of opening the later dungeons, but... What is it a resistance against? They never say. I'm not even sure what is wrong once you get rid of the Twilight that the average citizen could possibly be aware of and make any attempt to fight against. Other Zelda games will tell you where the monsters came from or create an image of a world that functions around their existence and is impacted by it, but I have no idea if the Bulblins are supposed to be an actual invading force or just the equivalent of like, the local bandits acting up. And the problems that were there seemed to be largely unnoticed by everyone not directly impacted. The residents of each location mostly keep to themselves, so the people all come off as very isolated, unaware, and blind to the world around them, to the point of creating dissonance. There's the giant barrier that appears around Hyrule Castle for half the game, visible from basically everywhere and right in the busiest town in the whole series, and surely someone has to comment on that somewhere, but I couldn't tell you who or what. There's very little sense of community anywhere in Twilight Princess, which I think is interesting. Ordon's population is decimated early on, Castle Town is crowded and impersonal, the Zoras and Gorons don't really get actual settlements with homes or anything, and Kakariko is a ghost town. By the way, the reason Kakariko is a ghost town is because all of the residents aside from Barnes, Renado, and his daughter were killed and turned into monsters. This is stated in one line and then never brought up again in any way, even indirectly. It's so weird.
And also there's Hyrule Castle. The entrance to Hyrule Castle and the whole dungeon itself have such an off vibe in Twilight Princess. I think he brings this up in his Twilight Princess video actually, how all life suddenly just disappears when you get close to it and there's a lot of space with no real purpose. It's like stepping into another world in the middle of the busiest city in Hyrule. Other versions of Hyrule Castle generally try to stick to a semi-plausible layout, but this one is built really uniquely and nothing like any other dungeon in the series. When you go inside the main entrance it immediately hits you with this big room with zero reachable exits, but there's this tiny ornate wooden staircase to nowhere sitting off to the side. It's just bizarre because these things are part of the architecture, they're not game elements dropped in to the space or consequences of the castle being destroyed or transformed. It's actually just like that. And outside it's completely silent and inside you have the music that really emphasizes the weird emptiness of the place. It also doesn't feel like the same location as the earlier visits at all, the scale of the place feels so much smaller despite all the massive empty spaces. It's got to be my number one example of a place in a video game that just feels off.
