That tool sounds SWEET!!!!
Using the dial caliper as a depth gauge definitely will introduce deflection error in the readings but it is over such a short distance that it is not a big deal for going down to the hundredths.
At first, I just set the gauge then push it down, as the tip of the caliper rests on the machined spring seat, until the tail of the caliper evens out with the bottom edge of the retainer. At that point I can move the caliper around to see if any deflection has caused me to eyeball it wrong. It always works out and the measurement is repeatable, I have moved the caliper about .010" and then re-measure again, and I will not be able to line up the retainer with the caliper no matter how I hold it, so I am sure it is within about +/- .003.
Even after all that, because it is not the best tool for the job. I put a magnet on the bottom side of the retainer so that I had a firm edge to go from and the magnet squared off the calipers to avoid any deflection. And BTW, The heads and valves are clean, the valves I was checking have even been lapped so everything was sitting tight.