:point_up_2:t2: exactly this. Those two things are logically different: I should not see configuration in places that are meant for my notes.

I do think think there is a way around this, while still getting to keep all of the advantages: make the notebook a special case, hardcode its name and hide it.

More precisely: imagine you set the name (and I do mean the name, I don't care about the ID) of the notebook to ce8e849c-b6a2-4f19-b2b1-9a4f9b4f57ee, or some other random guid. (Please don't use all zeroes, that's just asking for trouble.)
No need to implement notebook or note hiding - just hardcode that notebook to be hidden.
Also no need for special notes with specific names - Add a menu item saying "Customize CSS" (or maybe "Customize CSS for this particular instance" that will open (or create) a note, with a hardcoded name, in that notebook, and display its contents in a 'edit settings' window/dialog.

That way, it could internally be a notebook for syncing purposes, there would be no issue of it being displayed among your other notes (because the notebook would be hidden) and no issue with specific names (because that'd be hidden as well, and handled when a user clicks on the 'Customize CSS' menu item.)

I think this is a bad idea from the UX point of view. Having to see an option on every single note, while that option will be used by a fraction of users, for a single note among potentially thousands you create in Joplin, would just be confusing and superfluous.