If windows didn’t exist, linux would dominate with the problems you describe, and we’d still see this meme, but advocating for FreeBSD instead.
That being said, I like them both. It’s been a while since I last used bsd, so I think it’s about time I give it another spin.
Depends on your OS, but symlinks can do that for you - file exists once, but multiple “files” link to it. The application (torrent client) doesn’t care.