A competent military deployment is yes and no. The captain and many of its members have served in the military, but the captain is free to get his crew from anywhere he pleases (within reason) so some are technically civilians. For example, if the Hawaiian rock monster ends up teaming up with them. His ship is likely part of a specially listed group that doesn't follow all military regulations. If he promotes someone to XO on his ship then this doesn't mean they'd retain this rank and go to other military deployments, and vice versa. The military could respect his judgement and transfer the credentials to the normal military, but it's not required for them to do so. He could go to an admiral say ask permission to promote someone and if they agree then it would be valid and not just after the fact.