We had a brief discussion back in October 2024 whether HeaderBar should be a normal layout container in the scene graph, or whether it should live somewhere else (for example something like Scene.setHeaderBar(), analogous to Scene.setRoot()). It became clear that we wanted HeaderBar to be a part of the scene graph, because its capability to interact with the rest of the scene graph is one of the main features.
This naturally exposes HeaderBar to the same question that the rest of the scene graph has to solve: what to do in case of an overconstrained layout? Layout containers have different (but well-specified) answers for this question. In your example, you're using a StackPane as the root layout container. By default, StackPane will center its content if it can't be resized to fit the available space. This behavior can be adjusted with the StackPane.alignment property: set to TOP_LEFT, the HeaderBar in your example will stay where it is. The way I see it, there's an easy solution: use the scene graph the way it's designed and meant to be used. If ControlsFX wraps the scene root in a StackPane, but doesn't set the content alignment to TOP_LEFT, then that's a bug in ControlsFX because it changes the way the scene graph is laid out.
