I think the confusion lies with the Naval Academy CIS portal. It clearly states: "These are all the application materials that are a part of your Candidate Application Packet. A date displayed next to the specific form indicates the date it was processed by the Admissions office. An "N/A" indicates that it is not required as a part of your application. If you are also applying for an NROTC scholarship, some of the information you have submitted for that program may qualify and be used as completed USNA application documents. Additionally, some USNA application documents may be used to complete NROTC application elements. If you have any questions please e-mail your Regional Director listed at the bottom of this page."
Upon emailing the regional Director they confirmed they are indeed separate Applications and there is no cross connect between the two. What this paragraph is saying albeit not very clearly in our case was you need to get those for USNA so keep copies and include with the NROTC application.
USMA does it a little differently and someone help me here, but those qualified candidates not selected for appointment are automatically offered an Army ROTC scholarship. I do not recall if an application for AROTC is required for those not appointed. I do not believe Navy has this policy not sure about USAFA. So I think Army is the only service to offer this scholarship to qualified applicants that failed to receive an appointment. Anybody jump in here to correct this if I am wrong!!