The difference is that the law only applies to ships that carry goods or passengers from one US port to another. Ships are allowed to (and often do) call at multiple US ports on a voyage, they just can't unload goods in one US port that were loaded in another.

For instance, the ship could have carried cars made at the Kia and Hyundai plants in Mexico to the US, and also loaded cars made at the plants in Georgia and Alabama for delivery to the Middle East.