Placing unique Service requirements (or weapons system deltas) in an annex is a common practice in both joint and non-joint programs.  Generally, the Service producing the weapon system uses the main body of the document with the annex reserved for Services that would like to have unique requirements or additional orders.  In terms of the acquisition strategy, there will be two as the principals are the Navy and Air Force.  The Air Force must develop an acquisition strategy that certifies that the modified Navy weapon can meet Air Force needs with an appropriate Acquisition Program baseline (APB).  Second, the Navy must have its leadership chain agree that Navy's Acquisition Strategy can meet both the Air Force’s technical modifications and schedule.  Perhaps, the most important document, in this case, is a Memorandum of Understanding/Agreement between the Services that identifies roles, responsibilities, and important deliverables.  And yes, each Acquisition Strategy should have this Memorandum of Understanding as an additional annex.