UPDATE 2
So I called Apple back. I got forwarded to a manager. This time a knowledgeable lady who looked over my case and said "Yea this isn't right." We put confidence in our shippers and we shouldn't punish you for it. So she is rush processing a new Mac Pro and sending it with faster shipping. Should be here next week sometime and she's going to credit my account $200. I feel a bit better, but it was just an overall nerve racking process. Oh well.
First things first, ALWAYS speak to the manager in complicated cases... this is a good case in point. Apple has always been good to me when I spoke to managers (they have much more control to do things) and this is another good example of apple support.