Maybe there's a way for the narrative or game design to gloss over the fact that everything's so close together? At the end of the day, the tweaks to this massive design component of the Larian style are going to have to be small, but there are many ways small things can be added to create an illusion of distance/time/scale/scope.
For one, I can say that I don't like that the mini-map/fast travel map is a lot like the map from DOS2. I would prefer a more stylized map rather than a very "literal" map. Go all high fantasy for the fast travel map design, put it on parchment with ink and little scribbles when someone tells us to mark something on our map like Zorru or when we pass a check concerning a location or if a character wants to add commentary... even adding areas to the fast travel map that we can't go to, like
https://en.wikipedia.org/wiki/Here_be_dragons This means that every time we use the map, we are reminded that this world is not a tight, static board, but is a real world that requires a map with some scale, and we are only traveling to the locations relevant to us in a much larger world, like in BG2, or any RPG with an overworld map that separates zones. This would work especially well with the Underdark, where we are walking over land bridges with supposedly dangerous terrain beneath. It would also allow for more lore references on the map. GM4Him brought up slicing up the map... maybe to preserve the seamless transitions of the theme park style, the fast travel map can imply that we exist in a world more like what GM4Him is suggesting. Having said that, GM still makes good points about being able to see certain locations from others in that style of map (Grove and Goblins). Maybe the druids employ some sort of nature magic to cloak the grove in trees and vines and tall grasses? Or the shadow druids have some other kind of illusion magic (I'm not a dnd lore expert).
If the game can't handle dynamic lighting (something I would really like for Baldur's Gate 4 if we get it), maybe give us a clock or sundial we can check by pulling up the map or pulling up something else. It might not even have to be based on real-time, but instead on a combination of short rests, HP, spell slot consumption, combat encounters passed, and major story moments passed. Fog is not a bad idea, but on its own, I don't think it will accomplish much, as Flooter mentions. Flooter further makes a good point that it feels like those medieval villages with rehearsed lines sometimes. Maybe giving more varied lines based on context could help to break that sensation a bit? Looking back at DOS2, you can only hear, "Keeping it together Bree...," so many times while going to the area over and over again before your immersion is broken and you are losing your mind. The NPC chatter has been a meme (and not always in a good way) in the DOS subreddit for quite some time. Just google "dos2 npc meme" and the bulk of the reddit search results are people complaining about npc conversation repetition (Cheese merchant in DOS especially, with all due respect to those who like the Gorgombert).
Maybe characters with low strength, dexterity, or athletics can remark on the amount of traveling being done on foot (Potential for being annoying though).
Also, how big is a Nautilloid? Is there some justification for its size resembling a substantial distance on the map? Is a nautilloid bigger than the crypt, or the grove, or the temple? Is it also big enough to be as big as a substantial chunk of the road to Baldur's Gate?
Should we have a day counter for how many days our journey has taken, based on each long rest? Maybe that would help when a character says that a place is one or two day's journey away. I don't think dnd has names for the days of the week like the Elder Scrolls (Morndas, Turdas, etc.), but that could be a way to make it more immersive.
The camera can also be used to give an impression of distance/scope/scale. In places that are smaller, maybe the camera closes in a bit more to give character focus and a bit of mystery to the area. When we are walking across a giant ridge, maybe the camera can be encouraged to zoom out and to the side to show us how massive the world is compared to our characters? A bit concerned about taking camera control away from the player though.