Its about time you solved for adding a layer that does not populate in every scene and must be manually turned off.
At present we can use Super Section, but that makes a section and a new scene as well. We should be able to do with simply by having the option on the Layer Manager to add a hidden layer.
This might be a nice built-in addition, though there are several layer manipulation plugins/extensions available that already do what you ask. Do a search on any of the plugin source sites.