It is not so much the Navy "promoting mass transit" as you assert as it is Navy calling SHA to task for not studying transit alternatives as modern practice generally requires. But you are correct on one big thing, and the main reason for the letter: the Navy has no interest in ceding property for the project, which would compromise some of NSA Bethesda's force protection requirements.
And, short of an Act of Congress or the Pentagon overruling the Navy, they are not required to cede or sell anything to SHA.