taxes etc on registering a boat in St thomas

I've registered several vessels in USVI and tax has never been an issue. Insurance is something else entirely and terms are agreed with your insurer/underwriter.

Your USCG documented vessel is registered with the federal gov't and St Thomas would be your home port. Very easy to change.

Most underwriters don’t look at the port shown on the doc but at where the boat is actually kept and used as shown on the insurance application and attached questionnaire.

the port list on the documentation can be pretty much anything you want it to be which is why you often see boats with landlocked “port” like Atlanta Ga.

Insurance goes by coverage area. Where it's registered I don't think has much bearing. If Puerto Rico is excluded for coverage, even registering it in St. Thomas would still exclude it from P.R. I would be asking this question to insurance agents.