The total level of compression we're talking about here makes the altitude difference almost miniscule. Standard atmosphere sea level pressure is 14.7 psi, 6,000 feet (where I live) is 11.8 psi, and 10,000 feet is 10.1 psi.
Compare those numbers to the final pressure under compression (I'm not sure what it is, but even if it was only 200psi...), and the difference is small. That is why a turbo charger works so well at altitude; not only does it give you additional power, it basically makes up for the loss as well. 4.6 psi is a small percentage of the final value.
As someone above already said, once that piston moves only a little bit, you are already back at sea level pressure.