The MOD works on the basis that it is a law to itself. Precedents include its SCS confirming that issuing an order to suborn UK Military Airworthiness Regulations was lawful. A CS disobeying such an order was committing an offence. It even managed to pressure the HSE to continue with the prosecution of MBL in the face of unequivocal evidence that it was innocent of the charge. The rules are for little people.