When screwing two pieces of wood together, you want the second piece of wood, in this case the neck, to be threaded and the piece the head of the screw or plate is pressing against, the body here, to allow the screw to rotate freely within it so the screw pulls it tight against the neck when tightened. If it threads through both pieces, it not only places a lot of strain on the wood as the screw tries to pull them together, it could push the neck away from the body slightly before threading into the neck. If this happens, the screw will hold the neck away from the body(small gap) even when tightened and could strip the threaded area out of the neck if overtightened to try to pull the pieces together by force.
Have the holes on the body drilled out slightly so the screw drops through freely then just spend a little more time making sure the neck is aligned when tightening it.