Right now they do not add automatically, just manually in the preflet. I did think about adding automatically for a future update. I would need to add the ability for the server to save changes to the notification settings file (it only reads now), and add code for the preflet to detect and reload changes made by the server. To do in a future phase.
The setting (or future settings) here in this tab are per application, so the mute is specific to the application selected.
Yeah a bit more explanation is warranted. I am envisioning in a future phase to have other application specific settings. For example being able to disable the notification timeout or specify a different timeout than the system default. Or perhaps choosing a different screen location than the system default. Then it is more complicated than just a simple enable/disable option. I would also change the application list to a ListItem view, and do something similar to SoftwareUpdater and have the options for each app displayed as extra text lines and add an icon.
And about the use of the term "mute". In future (again) will be the ability to view a history of all notifications received, or some type of shelf for notifications that timeout (user does not click to dismiss) and get sent to for viewing later. Like MacOS or Gnome. So "mute" does not disable notifications, it just prevents them from being displayed as the pop-up. The notifications will go directly to history/shelf. So you can "mute" notifications and you won't see them pop up but will see them in history. This to me is different than "disable", which would not allow the notification at all, so would keep it from showing in a history or shelf.
But since we do not have a history or shelf yet, for now mute will be in effect the same as disable. In a future phase is planned a deskbar tray icon, where you can "mute" all notifications at once. So you will not get any popups, but any notifications will still go to history/shelf for viewing later. That would be different than "disabling" the notifications, which totally shuts the server off. I hope that makes sense.
Edit: We had used the phrase Do Not Disturb before. Would that be better than mute?