You're right, Yorktown is a conspiracy theory... btw, here's a link that shows some of the early efforts in creating the Seal... http://www.greatseal.com/committees/firstcomm/
This arrangement of the 13 stars was done at the request of George Washington to honor Haym Solomon. Solomon would raise the $20 000 dollars Washington needed to march his army from Hudson Highlands (New York) to Yorktown, bringing the war to a close, and keeping Washington from being penned between two armies.