So in the sample capx (which has the JS icon located in the Projects>Objects window on the right) if I open a new layout and then "Insert New Object" the JS icon doesn't appear.
It doesn't appear, because it's already added to the project! It's the same with many other objects which you can only add once - Mouse, Touch, Browser etc.
Once it's added to the project, you can use in the event sheet. But you can't put "JS" onto the layout.