The confusion may come because you do clear into the USVI at the ferry dock and then again into the US proper at STT airport. There are two reasons. First is that arriving in the USVI from ther BVI is moving from one soverign teratory to another which requires a passport and possibly a visa. Travel between the USVI and the US does not require a passport. Then the USVI has different duty and agricultural regulations from the US proper.

Travel is fatal to prejudice, bigotry, and narrow-mindedness, and many of our people need it sorely on these accounts. - Mark Twain