The most relevant things in this case is that the prez is classifier-in-chief and record-declarer-in-chief and can classify/declassify and declare a record at will. He doesn’t need permission from subordinates, nor does he need to follow the guidelines his subordinates have to follow.
The order referred to here only means that copies are kept at DoD, but other extant copies are still gov property, managed securely, and must ultimately be returned or destroyed via established process. The fact that a copy is at DoD does not absolve gov employees or contractors from those processes.
However, again, the Prez doesn’t need to follow any of that.
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