This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate.

This is not a contracting or an acquisition question.  The answer to your query must come from the cognizant USAF security office.  Logic tells you the security people responsible for the task and its execution should be the cognizant office rather than the office that is only the contract vehicle.  We believe you need to inquire with your security person.  We think that office would be responsible.  The office receiving the MIPR (and task requiring a DD 254) would want be assured that all security issues have been properly determined and adjudicated.