"It should be straightforward to place two straight pieces of wood against the top surface of the stone and the bottom surface of the stone and thereby establish that the two surfaces are reasonably parallel to each"

You can see in figure 2 of this article that this is precisely what I did:

[www.egyptian-architecture.com]

There is no doubt the stone is very close to 1 cubit in vertical thickness. I suspect the 546 mm dimension they quote on the NMS website was not taken perpendicularly to the flat top and bottom.