I also don't think the people in charge at the TSA are so stupid as to not have considered that someone might alter a boarding pass.

I'm reminded of a post here a few weeks ago, I don't recall the subject exactly but I believe it quoted Henry Kissinger, who said until you are on the "inside" of these agencies, you have no idea of the things they know, and that many things that don't make any sense from an external viewpoint DO make sense once you have all the information.