Currently, VSTO/COM add-ins are loaded and started automatically when an Office host starts. It allows adding capabilities or trigger actions without the user having to do anything.
However, office-js add-ins are only loaded in the document after the user triggers the loading the runtime, for instance by clicking on the add-in ribbon command. Setting Office.addin.setStartupBehavior(Office.StartupBehavior.load) is an effective way to load the add-in every time the document starts but it only applies to the current document. There doesn't seem to a way to apply it to all new and future documents.
Ideally, there would be a way in admin.microsoft.com to specify that an add-in must be loaded every time a new document starts (or an option in the manifest).