Correct. Traveling between Schengen countries is, for most intents and purposes, the same as traveling between American states.
The thing about the military flights is, you're confusing the border guard and telling them something unfamiliar. Just show them that you've got enough money to buy a ticket back to the US after 90 days. That is far less shady than "I am relying on this obscure thing with the US military to which I once had a connection".
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