Murdock,
I believe there is a thread on this in the BVI forum. But we just returned from a charter with Waypoints in St. Thomas and did this for the first time. We loved it and it was easy. Of course the boat has to be properly registered (I believe all Waypoints boats are). Here are a few comments on the process and the path we took:
Arrived at St. Thomas airport around 2 PM and Waypoints cab driver was at baggage claim to meet us and help with luggage. We were at the base 8 minutes after departing the airport
Our boat was ready early for a sleep aboard and provisions came shortly after we arrived. Folks at the base were great.
We had an early check out the next morning and were enjoying lunch and a drink on Honeymoon (St. John) before noon - about a 1.5 hr motor. We had our crew meet us in St. John that day - they took the 3 PM (or 3:30) ferry from Crown Bay (5 minutes from airport) to Cruz Bay, St. John. We picked them up in our dinghy. We liked this because it gave us time to do extra provisioning, set up the boat and check it out without the crew hanging around.
The next morning we had a 50 minute motor to check-in at West End. Customs opened at 8:30 and I was second in line. I completed the SailClear information before arrival. Process took about 45 minutes, but would have been less if I had not forgotten to bring the CRVL form - fortunately, my wife texted a picture of it from the boat and that satisfied the customs officer. After more motoring (and a little sailing), we were at Cooper before noon, and all of our "easting" for the trip was done, so we sailed the rest of the time.
We had a 6 night trip (plus the sleep aboard and had plenty of time to do the full loop (Anegada and back)), although I would have preferred 7-10 days. We sailed back from Anegada Monday morning planning on checking out of Great Harbor, Jost, then spending the night. However, that was when Beryl came through with some southerly swells.
So instead we went straight to Jost and just checked out, then headed to Maho on St. John for a more protected anchorage. Check out of Jost was a little slower as power was out and I had to redo everything I already did on SailClear on a written document. Plus the Customs officer came and went. It should have taken 15-20 minutes if they had power. Checking in via ROAM was super easy (be sure to load crew and boat well before), then process takes no more than 5 minutes, all done from your boat. It took an hour or so for Customs to respond that we were clear. Also, if you are at Francis/Maho, get a ball closer to Francis for cell service - no service tucked into Maho, and Maho Crossroads did not have wifi.
While this is certainly not how I would have planned it, I thought it was cool that we could leave Anegada early that morning, check out of BVI and be back in the USVI checked for a late lunch.
I will also repost this on the BVI forum.