There's already a similar Idea regarding configuration per environment, but this one is slightly different: very common plugins can be used by several apps in a factory, but each may need that different configurations. An example of that can be the Camera or Geolocation plugins, where the permissions labels (CAMERA_USAGE_DESCRIPTION, PHOTOLIBRARY_USAGE_DESCRIPTION, etc) may need to be customized per app. 

A nice way to handle there per app variations could be the client app setting those in its own Extensibility Configurations, that would override the json defined in the plugin's Extensibility Configurations.