I am not sure why you would have an issue with provisioning in St Thomas? Ther are multiple companies that will provision for you in advance. There are also multiple grocery stores. Even big-box warehouse stores for large groups.

As for the customs fees. This, unfortunately, is a pay me now or pay me later. That money is gone whether you charter in the USVI or the BVI. Us based boats pay $16 a day, BVI boas pay $6 a day. So seven days on a USVI based boat will cost you $70 more per person per week. The Ferry is a $90 round trip. The environmental and security fees are the same whether you ride the Ferry or a USVI based boat. You will pay slightly more in Park Fees and the port fee regardless. Your other option is to fly into Beef Island. This will normally be even more expensive than the ferry.

None of these costs include a night in a hotel on one end or the other if the schedule doesn't work out. Let alone that lost time. Then there is St John. The Crown Jewel of the Caribbean. Most BVI boats never get to spend any time there. The value of getting off the plane and onto your boat in under an hour is hard to monetize.