Sliding the tempered glass sheet I used for the initial trials and B-size Spirograph plots under the Z height probe eliminated the plywood benchtop’s small-scale irregularities:
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?
The Smell of Molten Projects in the Morning 
It’s astonishing to me that the defect moves with the glass — I would have been certain the glass was molecularly flat in its unstrained condition and just had a speck of dust underneath at the center of the mountain…
I think you can have either flat glass or tempered glass, just not both at once. Although I assume the sheet is tempered, I’m unwilling to cut into it just to see if it explodes into Chiclets.
The reflection of the overhead shop light shows a teeny barrel distortion over the lump that may consist entirely of confirmation bias.
I seem to remember a polarized light trick to verify temper; sandwich the test piece between two sheets of polarizing film (crossed, I think), and if it’s tempered, you get a cross pattern.
Optically flat pieces of glass tend to be really thick; my 5″ flat is probably 1.5″ thick, if memory serves. Sheet glass is usually produced by the “float” method; molten glass is set on a bed of liquid metal (don’t recall which). It’s kind of flat, but not very. Making optically flat (1/4 wavelength of light or better) takes a fair amount of care; the usual technique needs three surfaces; make A conform to B, B conform to C, and C conform to A. When they all agree, you have 3 flats. (BTW, this kind of glass is carefully annealed.)
Mmmph, it looks dead black. Maybe there’s an overlying grid on half-foot centers, but it’s hard to say. If I can continue to not drop the sheet, we’ll never know …
A bit of searching the web says: Try one sheet of polarizing film and look through the glass. Roll marks or tong marks will show in polarized light. Modern stuff is now identified at the corners with some kind of stamp. The same article verifies: tempered glass isn’t going to be very flat.
Looked at my optical flat: 150mm diameter x 55mm.
If I ever drop that sheet, it’ll fill the Basement Laboratory with razor-sharp shards: no internal structure, no clamp marks, no stamp, no nothing. On the other paw, it might date back to the dawn of float-glass technology, making it both reasonably flat and highly stressed.
Hey, it might even be a Valuable Antique!