The holes, as seen in the video, serve only as a reference for the subsequent square-shaped shaping work to allow the subsequent insertion of the square rulers, they serve as a sign to identify the point to be shaped well
The beams look “cut short” but in reality they are not because they go all the way through the hull. The drawing shown in the manual, as you can see, is just an excerpt, an explosion of that point, a kind of section. On the other hand, from the photos of the finished ship, you can see that they go from one side of the hull to the other