I can’t say I’m privy to the reason, but from my work in image editing I can tell you that anytime you are merging images you need a clean join line for the most seamless edits. What using the set and just adding the rest would end up doing is creating a join line down the middle of the ship. What they did was to make the join line in a place that leaves the largest section of the upper surface as a single image. It leads to be best quality end product. Also, I don’t know if they spent much time detailing the top of the live action set so it might have been far less detailed and the may have done it for that reason as well.