Deck height ain't nuthin.
Deck height is not part of the stroke measurement.
You bring the piston up to TDC, zero the tool , and measure the travel to BDC. All of that assumes the tool travels straight the same distance as the piston. If the tool was at an angle to the bore, a 4 inch piston travel will produce a dimension that is greater depending on the angle.
If you are not straight over the piston with the tool any angle will produce other results.
In an angle plug application, fluid works best without all the monkey motion.