Tha Jones Act merely applies the same anti-cabotage rules for the air-space, to the waterways.
While, on the face of it, it looks like a commerce regulation, it is also a safety preecaution, helping reduce espionage, and sabotage of coastal waterways, and forcing a higher standard of care in them.
International waters is the ONLY place raw sewage can legally be dumped overboard, by US law. Getting to the point that will include ballast waster. "So what?", some might ask... Many nations just disallow it while in-port, in bays, estuaries, etc. take a good look at the Brazillion Olympic games, for the water-quality and pollution problems that the Jones Act has helped prevent, in the US.