Where to charter from.... You will find as many opinions one way vs. the other so really no right or wrong answer.

I think I would go with the boat that is best for you. The other logistics are essentially a wash.
(a) Yes - you will have roughly one day less in the BVI. But you will pick up a great experience on St. John instead.
(b) Cost of ferry "fun" is about the same cost as the cruising tax++ to bring the boat into the BVI. But as noted this might be changing to a little bit unknown at present.
(c) There is no complexity to check into/out of the BVI. The charter base on STT will walk you through it and it is frankly a non event. So don't let that be a determining factor.
(d) Probably less can go wrong if you start in STT. If you are flying in/out of STT already vs. you have a choice of flying either EIS or STT then way less can go wrong starting in STT. Especially on the way back. Often times if you are returning the boat on Tortola and you need to get the ferry to STT there is a good chance you will need to get to STT the day before in order to be safe catching your plane. So there goes a whole day of your vacation that could have been spent on the boat had you chartered out of STT.

So IMHO, the determining factor is the boat and the price of the boat.