Tom,
Mine don't have the flat area, the dome starts at the skirt, illustrated below.
Now, I do know the dome height, this was a published figure from JE, so it's easy enough to compute the deck height by measuring on top of the piston in the flat area you see (my "massaging" didn't remove any metal there, just smoothed the edges), subtracting the dome height (after converting it from decimal-inch to metric, JE uses inches) and then comparing that "deck height" to the top of the cylinder.
So how would you set up to do that? I suppose you could set up a pair of gage blocks on the cylinder top with a depth gage laid across them, then zero the dial indicator at the base of the depth gage (the same plane that the gage blocks touch) and do the math that way. The nice thing about the red "bridge" style gage is you can zero the indicator on a flat surface then rest the ends of the bridge on the cylinder top and measure directly. But the depth of the bridge had better be greater than the dome height and a long-stroke indicator would be required.
Decisions decisions.