Compression ratio vs Porting

If I had to guess it would be that the cylinder volume is greater than the port volume. So as the piston pushes with the valve open, there is still pressure being built, just not as much as if it were closed. Pressure is flow restricted so piston creates pressure, port creates restriction. Somehow I think you knew this.....

you are correct that valve operation (timing, lift and duration, etc) have no effect on STATIC compression, this is because it does not take into account above, its simply the compression given by stroke/bore/head gasket/etc.

When you get into DYNAMIC compression the game changes. You are now looking at what the actual effective/dynamic compression ratio of the engine is. If you have 10:1 and put a cam with no overlap it is going to have a ton of cylinder pressure because you were able to fill the hole with little to no loss thru overlap or a valve being open. Now with a big cam and a ton of overlap your cylinder pressure will be less due to the valves being open and overlap, your effective compression just dropped. With this your static compression hasn't changes, bore/stroke/comp height) havn't changed BUT because of a bunch of factors based on cam, valvetrain and heads your effective has changed, and in the end its the one that matters...