The "arrangements, and lines" drawings show the cockpit detail, but the deck layout indicates a "continuation" of the deck planks inside the cockpit, with a grating, thwartships, in the after end. Would the cockpit deck be "lower" than the deck outside the cockpit? Good question. The plans don't show it. If in fact this was done, then some form of scupper would have to be built in, to allow drainage of the cockpit. Photos, on the "net" (I don't have the links) show one of the other N.Y. Pilot schooners, with the same cockpit structure. The cockpit enclosure is narrow vertical planks, with a railing set on the top. There are several small cleats at the inside forward end of the structure, but deck level isn't clearly shown.
America, which was designed after a pilot schooner, has a very similar cockpit, this one set into the deck, and with grating throughout.
America was, by design, a yacht, not a work boat, but was constructed at about the same time as
Phantom. Without photos of
Phantom, I would suspect that common practice was a "recessed" cockpit, so carving out the hull blank, at the cockpit area, to represent the lower cockpit deck is probably more correct than not. Providing some depth, in the cabin, is probably a good thing to do especially if the door, and hatch are open. I concur with bronze pintels, and gudgeons, on the rudder,and hull, at least below the water line, and more than likely, because they were probably cast, above the waterline also(I don't see bronze castings for below, and iron castings for above, time was money then, as it is now). Yes, I would call this a "beginner's kit", as it is an excellent introduction to wood model ship building. The hobby does get more involved with detail, and historical accuracy, but for now, this kit will produce a good looking finished model. which will draw attention from most all who visit you.