If you create a custom notice that is not an overdue for your branch the system still sends the notice for 'all libraries'. This is not true for slips and overdues which can be customized on a per branch basis. Either this is a bug or if it's a development it needs to be clear on the notices & slips page that you can't create certain notices for your library.
Checking in to see if this is a bug or an enhancement that needs better documentation.
I don't believe this is the case anymore, the wiki states: As of 3.16, all notices should be available to all libraries, or may be branch specific. Likewise, all notices should respect the HTML flag. If you find an exception, please file a bug report. https://wiki.koha-community.org/wiki/Customising_Notices_and_Slips If there were new notices introduced since that don't work correctly, we should file separate bugs for them.