Clearing into the USVI on a US boat with US crew is a phone call, if you have nothing to declare and you do the SVRS online. No biggie. Check out SVRS online if you sail with the same crew consistently.
As for clearing into PR from the USVI, it is because the USVI are duty free ports and PR is not.
You can fly (or sail) from PR to the US nonstop without any formalities in the US when you arrive, because you've already cleared into the US in PR, so it is basically a 'coastwise' voyage, just like between states.