Yes, true, the effect is the same. A ship from overseas passes by PR with goods for the island. It harbors there. It continues to the mainland, now it’s in violation of the jones act since it’s transporting goods between US ports. What are the huge cargo freighters going to do? Unload everything at PR? No. They’ll pass and unload at the mainland.
Minor nitpick: they are not technically in violation of the act unless they actually onload cargo in PR, i.e. they could just offload at PR and continue on to mainland. The end result is the same though as merely offloading is not efficient so the ships always go to the mainland instead.