Here’s a pic of the tray that I hope clarifies things.
The measurement we want is A, the distance from the floor to the top of the honeycomb.
If you put a depth gauge through the honeycomb you’ll only get measurement B because it hits the floor of the tray.
So instead we measure C and subtract D, because it’s easy to reach both.
The fact is, though, that A is supposedly pretty consistent from machine to machine, so you don’t even need to measure it on your own. Just zero your calipers at something like 1.37 or 1.38 and you’ll probably be close enough.