The physical elements might have been correct in their proportions, but these elements could be distorted on computers. This happens frequently with models where photoshoppers distort the Human form.
This distortion is visible in the screen shot. The deck pieces have been extended. In the original SD shot, the edges of the pieces fall within the beam. In the new shot, the edges of the pieces, especially for Deck 5, considerably falls outside the beam. The beam is the width of the hole.
As for the cutting beam, it was used to cut the hull to a certain depth. When the beam had completed its task, the beam was turned off and a grappling beam was then turned on to take a sample of the starship's hull.
What's more likely - that they resized one particular element of the shot, that was part of the same original model, or the beam (not the cutting beam, you're right) doesn't cover the whole piece in this frame?
"When you eliminate the impossible, whatever remains, however improbable, must be the truth."