We've been in Cruz Bay at least three times with IYC and other charter boats, including anchoring on the North side and docking twice at the gas dock for water and once at the Customs dock. If it were my boat that was in charter service, I'd want the charter company to tell you to stay outside at a mooring and dingy in.
The most challenging moment in Cruz Bay for us was getting off the Customs dock with ferry traffic and several excursion boats circling as they awaited our departure. The Customs folks had shoehorned us in to the point of our bow overhanging the transom of the boat ahead of us and our transom nearly touching the bow of the excursion boat that came in right after us. If we didn't have a bow thruster on the IP 420, I would have deployed the dinghy as a tow boat to pull the bow off the dock! Once off the dock, we had to make a sharp U-turn and thread our way through the heavy traffic--several excursion catamarans-- but that was the easy part, once we had way on. For some reason, we had arrived at the beginning of rush hour. Had we arrived 15 minutes later, we never would have been able to tie up at the customs dock. To OvO's comment, I'd say the issue is BOTH docking and traffic, unless you come in at a quiet time.
We've had sailboats for 40 years and are obviously more experienced than a lot of bareboat crews, IMHO. I remember sharing experiences with the crew from another charter as we shared a taxi back to the airport. It was a kind of "What did you like, what didn't you like, where did you go, what experiences did you enjoy, etc.," In the 45 minutes to the airport you can cover a lot of ground. This was 13 or 14 years ago on our first Caribbean charter and we noticed that there were a lot of bareboat folks with sloppy sail trim, questionable anchoring techniques, etc., In any case, we related to our taxi-mates our pleasant surprise at the $.85/ft slip fee at Spanish Town. We thought the big deal was how cheap it was, compared to our New England scene, but they were amazed that we docked the boat ourselves! That was the "Ahah!"moment for us and explains why the charter companies set some of the limits they do.
My bottom line on Cruz Bay: Don't dock at Customs unless you have a very good reason. If you do, be prepared for some tight maneuvering with restricted room and an off-and-on chaotic traffic scene. If you can find room, docking the gas dock (for water) is easier, but you have to check in with customs first (if you are coming from the BVI).
That said, you should discuss options with Skip at IYC, if you are inclined to be more adventurous than the average bareboater.