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I had the same question. Why would they be foreign-flagged if the are from another state?

Correct. Just like how most countries don’t allow foreign companies to operate domestic trucking or domestic flights.

It does mean places like Puerto Rico can buy things more cheaply internationally than nationally.

Similar to how Amazon (used to) enable sales tax savings by making it easy to buy from out-of-state instead of in-state.

The difference is that it's really rare to have restrictions on the vehicles themselves. An American company can register trucks (that have been homologated) or airplanes regardless of where they were manufactured; a Jones Act-compliant vessel must also be built in the US, which is a Catch-22.

Larger vessels are usually foreign-flagged for regulatory (avoidance) reasons.

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