There exists almost no US-other country shipping that is US flagged. The problem is that these foreign flagged vessels can pay slave wages to what are sometimes literal slaves, and we take advantage of it.

So yes, restricting the vessels that can use US ports even more will help US-flagged shipping.

Restricting people's employment opportunities doesn't make them better off.

It would eliminate the specific concern that a ship can't stop by PR on its way to another port.

It would make those restrictions more consistent between mainland and island US ports

A ship that docks at any US port can't stop by any other US port on its way.

Doesn't matter whether any of the ports involved are in Puerto Rico or otherwise.

So it's already very consistent (if stupid..), ain't it?