You would suspect wrong. In what's known as a care inquiry, such an agreement would have been acknowledged by MJ when a guilty plea was entered in open court, and the agreement itself would have been explored in detail with defendant in open court and on the record, per the MCM. The MJ has an obligation to determine if there was any coercion used by the government in obtaining the agreement. This wasn't done ergo there is no plea agreement.
It's not all that dissimilar to how a plea arrangement is entered in civilian federal court.
Your reasoning is overly simplistic. You obviously have no legal experience in the plea bargaining process. I understand why you can not follow this very complex plea bargain with your limited knowledge of the process.