Yeah that was a huge annoyance point in Hollow Knight as well if you want to 100% the game.
But it's also very easy to skip all that and just beat it.
There's also a fast-travel tunnel system that makes it a bit more forgiving.
So you don't have to run everywhere on foot.
There's even an NPC who comments on how weak you are for refusing to walk everywhere.
Pretty funny: so many references to the genre.