app.root - is actually root of an application, not the scene root.
In order to get scene root, you have to get first child of a app root: app.root.getChildren(), then you can get its children.
It is a bit weird I admit, that it creates magical “Untitled” entity as a app root, instead of just referencing scene root.
It could be that you were referencing app not the one provided in script create callback.
There is window.app, which is different thing, and only appears in launcher.
There were no changes to engine/editor between yesterday and today. Sometimes good sleep - is a best cure