Okay....Demon is correct, this does not always work. That's why I stated my uncertainty about it.
It works great in my application - I will not "guesstimate" beyond that.
Squish and cranking compression need to be verified. A physical compression ratio calculation would be a good idea, too.
Cranking compression is not the same as running compression. The sonic wave from the pipe will increase running compression, so it will be higher.
As for the question why porting lowers the compression: When you raise the ports, the piston will start compressing air later in the crank revolution than before. That means there will be less volume of uncompressed air to compress - resulting in lower cranking compression.
The pipe will stuff some air back in, which is why running compression is higher.
You might ask why FS porting would lower the compression...after all, that's not supposed to raise ports, right?
True, but I cut my exhaust port corners a bit more square than stock (I believe Paul does this, too). Changing the shape of that port from oval to rounded rectangle will lower compression, because parts of the port is being raised.