If your intention is to gain the best quench you can, it would make sense to check your piston at the quench spots, not in the center of the bore where the chamber is above the piston. Once you bring your piston to TDC, move your indicator to the quench sides of the piston near the edge and rock it inward and outward. This will give you some idea of how much rocking goes on inside the engine. You will see that it is sticking out of the bore a lot more than just .005 at these points. Yes, I have seen pistons hit the head with less than .040(true quench). Don't be afraid to really push on the piston as hard as you can to simulate the rocking, you still cant push it hard enough to match how much the connecting rod rocks it, but you will be safer in making your measurements there. Also, even at an idle with the engine running, the pistons go past TDC 10 to 15 times per second, so by the time you hear a problem it will be too late to do anything. At operating speed(6000-7000)RPM, you could take a bearing out or bend rods, collapse pistons with even just a slight bumping of the head. Just be cautious when pushing the clearance that close.
