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Try running the demo this:
https://gist.github.com/jewelsea/1441960 "Demo for understanding JavaFX Layout Bounds"
Not a direct answer to your question but hopefully it aids in understanding the relationships of these concepts and it is an example (albeit not a simple one).
Also review this presentation:
http://www.parleys.com/#st=5&id=2734&sl=57 "Interface Layout with JavaFX 2.0" by Amy Fowler
Particularly see the slide at 46 min and 20sec (and the following one which lets you know the useful tip that if you wrap a Node in a Group it's layoutbounds effectively becomes it's boundsInParent).
See also the Node javadoc on bounding rectangles:
Thanks John. I had read/watched all these materials, before posting the question. Some wrong descriptions (Region and Border classes) in FX 8 documentation confused me. After experimenting with FX 8 code/CSS, and reading more materials on w3c.org, eveything is clear. I have filed a JIRA for changing teh FX 8 docs.