The DoD is the civilian side that overseas the uniformed services.
If you look at the history of the DoD from its change from the War Department and Dept of the Navy, you see individual politicians and bureaucrats had a lot of sway.

Not every one is on the same team. During Vietnam, every Admiral, General and most above the rank of Lt hated Sec McNamara. Most people disliked Rumsfeld. As long as they are not impeached or fired by the POTUS they have huge autonomy to set the course THEY want.

The POTUS firing people in the "last few weeks" of his administration is not pettiness. It is a trust issue. He has the goods.