Working with Bounds Demo
There is a very nice public demo by Kishori Sharan that shows how bounds work: http://www.java2s.com/Tutorials/Java/JavaFX_How_to/Node/Know_how_three_bounds_layoutBounds_boundsInLocal_and_boundsInParent_are_computed_for_a_node.htm.
It uses a deprecated API, so I've fixed it and added it to our GitHub as chapter2/other/BoundsDemo.java.
In the following screenshot from this demo, there is a Rectangle with rotation and translate transformations, and a shadow effect:
The smallest rectangle represents layoutBounds—it's the position of original Rectangle before any other changes.
The bigger rectangle around it is boundsInLocal—the size of the Rectangle after the shadow effect, which spills a bit over the edges.
The blurred rotated rectangle is an actual image you will see after applying all described effects. The large square around it is boundsInParent—the actual size the Rectangle takes on the Scene.
I strongly suggest playing with that demo to get a grasp of how bounds work.