That is exactly what I am describing. when I put my hand in the engine block and push the tappets up as far as they will go they never hit the bottom of the valve. This is the scenario even when the valve has the spring seated properly. I did not shave off any of the tappet or valve either. this is odd.The clearance is so that the valves can seat completely. If the tappets never touch the valves, the valves will remain shut ALL the time, no matter where you turn the crankshaft.
Is this the situation you're describing?