Even though Arduino published different eagle file in purpose, i could understand. There are so many copies of Arduino board which infringe Arduino trademark. It is too easy for those factories to make the copies. If Arduino publishes different CAD files, the copy boards become different. For arduino, that is a good way to protect themselves.
Which would be fine with me if they did. However they should then clearly state that the Due product is not a true hardware open source product, unlike their prior products? I suspect that is not their intention, but rather just a matter of the published documentation not yet keeping up timely with actual production documentation used.
Lefty