What might be causing confusion here is that the USVI is a duty free zone. You can import things into the USVI and not pay duty, but that does not mean they can then freely be moved into the rest of the
USA and retain their duty free status.
This is why if you leave
Puerto Rico and sail directly to
Miami, you can skip
customs and immigration but if you sail from the USVI to
Puerto Rico or
Miami you need to clear customs.
All of which is interesting in its way, but certainly doesn't apply to a US built boat that is US flagged. Import duty is not at all handled like the EU's VAT.
A good
documentation agent can really help. In 95% of all boat sales, they do what you can do for free. Every once in a great while, however, something goes haywire. and having someone with experience can make the difference.