Yes somehow the doc mentions iOS only, although I don't see why it couldn't be used in other contexts including desktop apps. Or maybe I'm missing something and this scheme is useful only for iOS.
Though ultimately the format doesn’t matter all that much
Ideally we should follow existing standards as it means the app is easier to use, and we don't need to re-invent the wheel with a new standard. But if the only one is the x-callback-url and it's perhaps only used for iOS then indeed we don't have to follow it.
Personally I'd prefer something that maps directly to the API, so it would be something like what @tessus mentioned above - joplin://notes/ID