Regulating the "militia" as it were. If a ships Captain wanted to commission his ship to the US for the fight, he had to follow the rules.
So would it be if I joined up with the militia when called. I would be expected to follow the orders of those officers appointed over me.
This says NOTHING about civilian ownership of arms, ship board or otherwise, for those not involved in official US actions.
"no armed merchant vessel of the United States shall receive a clearance or permit, or shall be suffered to depart "
LOL!