I don't beleive they are going to charge you for a BVI based boat. Check with your charter company they will know.
Yes you can buy the forms when you clear out.
Yes the captain can clear everyone in on return.
I would not bother telling customs at the Ferry about a one day trip to St John it will confuse them. You will be leaving in a week by Ferry. The rest will be covered with the boat clearing in and out.
Jay