Exactly. You shave some material off the bottom of the head. This makes the combustion chamber smaller, raising your compression ratio.
Yes, I knew the exhaust exit ports were smaller, but as I read it didn't seem to be a huge deal. I guess I was wrong. I think I will take the time to port match, and do a basic port job outlined in the document you posted the link to.
It wouldn't take long at all to smooth off the rough edges that cause the most flow restriction. Specially since the valves are coming off anyway.