I took last night off.
Scott has confirmed that the system changes settings with the Matl Thk <> Focus Ht, anebed gives priority to Focus Height.
Maybe my using a light score to run the studies has skewed the appearance of the visual.
This weekend I might try again with either a deeper score or engrave. Maybe measuring the depth of the cut will help me visualize.
In the interim, I currently set the focal plane on the top of the material, so my first theorem is acceptable. It would also mean that if I remove the crumb tray for thicker work, I only need to make sure the top is within the 0-0.5" work zone and the red laser will scan and adjust focus to the top of the material.