Now with cross-wiki notifications T123570 there should be the ability to set a global default notifications for (most) wikis. The global default can be overridden on a per wiki basis. We do something similar with the meta deployment of global.js and, global.css, or similarly with user pages where if no local user page exists the default user page at meta displays.
Part of the design of cross-wiki notification preferences would be the ability to reset/purge existing settings so that the global default is set.