Since this trail is a military trial, I am not sure what rules of discovery apply. If he loses in military court, I am not sure if the appeals process can go into civilian court, ie the Supreme Court. Interesting that Judge Clarence Thomas made some oblique comments about the birth certificate controversy lately.
Since several of the charges are "disobeying an order", the accused must be allowed to make the case that the order was not lawful. Problem with that is that the particular orders were issued *after* he did not report to Ft. Campbell. The first charge, "missing movement" (not dereliction of duty, although that would be an included offense), is the one most directly tied to the One. But it really still involves disobeying an order (a movement order, in fact the charge specifies the exact commercial flight that he missed) so he should still be able to argue that the order to move was unlawful, because the ultimate order giver does not have the authority to issue the order (not being President and all). He must also be given the opportunity to obtain and present evidence supporting his contention. But ultimately, just as in a civilian criminal trial, it'll be up to the judge. However the Court (the panel of officers serving as the jury) will not look kindly on restrictions of an officers ability to present a defense, and they, unlike a civilian jury, can ask questions at trial, of either side.
The Manual for Courts Martial specifically mentions the authority of the order giver to issue the order as an element of it's legality.
If he should lose in the Court Martial, he can appeal, in fact it's automatic in cases where the penalty includes "discharge", to the US Army Court of Criminal Appeals. That's still in the military system, notice the .mil address. The next level of appeal is the US Court of Appeals for the Armed Forces, which is part of the same US justice system as the several US Circuit Courts of Appeal. Notice the uscourts.go URL. After that, an appeal to the Supreme Court is possible.
Military members have rights too you know, especially when charged criminally. In fact they typically have more protections than civilians in similar straits.
But, his only defense it that the orders were not lawful. He clearly disobeyed them, and did so deliberately. Proving that will not be difficult, if it's even necessary, it might be conceded by the accused.
Military court martials do fall under the review of the US Supreme Court.