PBW itself does no file checking, but Se4 does. We had concerns about this very problem and so have been working with Malfador from the start to identify and eliminate possible sources of cheating. Se4 does check to verify that the .plr file was created using the same executable that the .gam file was, and it also does some math checks to make sure there is no hinkiness with design costs and stuff. There are other things it does, but I don't want to give away to much information.
While it checks all these things I am sure that there are ways to get around it if the person is skilled enough and dedicated to teh task. There are always ways, and the cheaters always have the advantage in this arms race. But as new ways to cheat are brough to light we will try to get Malfador to fix them.
The one guarantee I can give you is that it will ALWAYS be possible to verify if someone is cheating. Because all we have to do is go back over the turn files and see if everything that happened should have happened the way it did. It's not always easy to do, it can take a lot of time and effort, but it's always possible to do.
Geoschmo