Am I missing something?
Oh yes. You are ignoring valve placement and operation.
A compressor's exhaust valve is open on compression stroke and closes immediately after. A compressor will keep pushing air out the exhaust valve as long the the pressure it creates is higher than what exists on the far side of the exhaust valve.
An IC 4 stoke engine has both valves closed during compression stroke and exhaust opens immediately after. The peak pressure created is a function of the ratio of cylinder volume difference between BDC and TDC. Change the ratio, change the pressure.
Milling the head and high compression pistons exploit this fact.
What may be confusing you is that the Compression test apparatus has it own check valve. The pressure of it's spring must be over come before filling the gauge's Burdon tube and connecting airway volume.
The cylinder itself gets full pressure on the very first compression stroke. The check valve only allows part of it to go to the burdon tube. (minus the check valve spring pressure, and the volume of the burdon tube and interface tube.)
The equations get more complex on successive cycles as the building pressure in the gauge reduces the volume entering past the check valve on each successive compression stroke until they approach equalization.
Much depends on compression tester design and where that check valve is placed on the apparatus. The closer the check valve is to the spark plug hole, the less effect the apparatus has on the chamber volume and pressures achieved in the cylinder. Not all compression testers are physically constructed the same way.
As important as what you test is how you test it.
If you are still not convinced, then put 10 or 20 feet of compressor line hose on the spark plug hole and place your compression tester at the end of it. Let us know how many kicks it took to match the pressure readings taken with the tester placed directly at the spark plug hole. Make sure the check valve moves with the tester.