Once you start to notice it, it becomes impossible to ignore. For me, I always notice how silly-short travel distances are. It's only a few minutes' walk between "major cities" in Skyrim, and it's one of the reasons I don't find any game (outside of VR) "immersive".
Some games do a better job by means of a different cheat (though I'm not sure you can even call it that). For instance, making it clear you're only accessing a very small part of the city. PoE2, among others, does a great job of this with a "city map" that shows you moving through many districts before reaching the spot where the story actually takes place. Distances, meanwhile, can be demonstrated by other means. The old Fallouts, for instance, had the in-game date swiftly advance while travelling in the overworld.
Some games do a better job by means of a different cheat (though I'm not sure you can even call it that). For instance, making it clear you're only accessing a very small part of the city. PoE2, among others, does a great job of this with a "city map" that shows you moving through many districts before reaching the spot where the story actually takes place. Distances, meanwhile, can be demonstrated by other means. The old Fallouts, for instance, had the in-game date swiftly advance while travelling in the overworld.