The system-noemail category (labeled "System") appears in the checkbox matrix in the notification preferences:

This is because AttributeManager::isCategoryDisplayedInPreferences() only looks at whether 'no-dismiss' => ['all'] is set, but system-email (appropriately) has 'no-dismiss' => ['web'], since email is disabled. If we do set no-dismiss' => ['all'], that would lead to email being both un-enableable and un-disableable for this category (ti shows that way on Special:DisplayNotificationsConfiguration, not sure if it has an effect in practice).

Either isCategoryDisplayedInPreferences() should be smarter and return false in this case (where all allowed types are non-dismissable), or no-dismiss should be interpreted differently.