The first height map looks like a mountain sproinged right up through the glass:
More red-ish means increasing height, more blue-ish means increasing depth, although you can only see the negative signs along the left edge.
The Z axis leadscrew produces 400 step/mm for a “resolution” of 0.0025 mm. The bCNC map rounds to three places, which makes perfect sense to me; I doubt the absolute accuracy is any better than 0.1 mm on a good day with fair skies and a tailwind.
The peak of the mountain rises 0.35 mm above the terrain around it, so it barely counts as a minor distortion in the glass sheet. Overall, however, there’s a 0.6 mm difference from peak to valley, which would be enough to mess up a rigidly held pen tip pretty badly if you assumed the glass was perfectly flat and precisely aligned.
Rotating the glass around the X axis shows a matching, albeit shallower, dent on the other side:
For all its crudity, the probe seems to be returning reasonable results.
The obvious question: does it return consistent results?