Just came across this. As I understand this means that I can edit an instanced scene's root node as much as I want, but the instant that I modify any of its children, even via a script, it has to affect all other instances of that scene.
So if I have a Person scene, I cannot move its arms separately from another person's arms. Am I doing something wrong here? Exactly how do Inherited scenes and Instanced scenes differ? I could explain how this relates to my code in detail, but it's so complex...