The Magic Kingdom ferry boats do dock at Ft. Wilderness. My family and I rode one several years ago on a summer night. The MK had closed and there was a huge crowd waiting for the boat back to Ft. Wilderness. It was quite a sight to see the ferry boat coming. We got on through a side entrance. When it got to FW, it docked nose first into the end of the pier and we got off over the front ramp. Talk about Disney magic!
I asked one of the FW/MK launch captains this summer is they still use the ferry boat for that trip. He says they do when there are a lot of people waiting and a boat is available.