While I agree that relative links aren’t the easiest to maintain, they do feel a bit more neural than paths relative to some core hierarchy. Relative links are independent of hierarchy and solely rely on the relationship between two Notes. Ideally, though, we’d scrap folder hierarchy entirely for a purely unique ID relationship. Luhmann was right to do this because then things are truly independent of their organization.
I can’t seem to reproduce this exactly on Windows or Mac. If I try to make a note at [[../test]] I get a weird “File Names cannot end with a dot or space” error on Windows or the “Folder already exists” error in Mac. However, I think you might be on to something with this, maybe Obsidian is trying to create a Note relative to the Vault root when it doesn’t exist and only correctly pathing relative to the current Note when the linked file already exists…
Is there any way to see whether this is a problem that’s planned to be addressed, if it’s not scoped, or if it’s not going to be fixed ever?
I’m a new user and this is hugely annoying. I was working on setting up a task list which I want to create nodes to future notes in sub-directories… And of course I ran into this 
It creates folders and files, but based on the root of the vault not the relative directory. [[./subdir/file]] from /root/category/file will create /root/subdir/file instead of /root/category/subdir/file.
I was pretty excited about the ability to create grey nodes for not-yet-done tasks… Since that lets me skip the annoying process of going and creating a bunch of new empty files just to go and link to them.
Edit: I’m on Ubuntu 22.04.04