There are other important differences between academic freedom in a DoD setting and a civilian academic setting. Much of the analysis done within DoD is about the organization itself--its structure, policies, leadership, etc. Most of the analysis done in civilian academia deals with organizations, policies, and people outside the academic organization itself. This means that as a general rule, critical analysis done under the policy of academic freedom within DoD strikes more directly at DoD itself than does critical analysis undertaken in a university. Very few academics build their careers through critical analysis of academia, particularly their own institution or their own leaders. But that's exactly what DoD academics do.

It is also true that most of the leadership in DoD, whether uniformed military or senior civilians, have not spent all or most of their careers in an environment where the value of academic freedom is inculcated. They understand "strategic communications" used to promote the messages and interests of the organization, but may not be as comfortable with public criticism of their organization from inside it. Given that, there is an amazing depth of tolerance for self criticism from DoD's senior leaders. I have long been amazed that the U.S. Army pays me to, with some frequency, tell it that I think it's wrong. That Army and DoD leaders can understand, tolerate, and value something that they may not have deep personal experience with says much about their sagacity.