Yes it does, but not every order comes from the president, nor does it have to go through him.
Those officers that 'ordered' LTC Lakin derive their command authority from the President as commander-in-chief.
Who's order/decision is/was it to keep the armed forces in Afghanistan? Who's order/decision is/was it to send additional troops there?
If the President (not a usurper) decides to bring all the troops home from Afghanistan...but the Secretary of Defense (or anyone else under his chain of command) orders the troops to stay....what happens? Who "wins" that order? The POTUS or the SecDef?
In this case, ultimately, the decision to send LTC Lakin originated from Barry's decision to keep and/or send more troops there. Those under "his" chain on command, implemented the specifics. That's essentially the argument of the Defense, and a clear one IMO.