"As I was trying to show, the top floor is the main deck. But if we travel up the side here we will have the main storage rooms for the supplies we may need to chart the course, take samples of rare plants, and store some bodies of monsters." The first floor was set up so that they could do the most with it and the ship builder showed this before pointing out the stairs to the deck of the boat.
"Then that is the way we should go." Scylla had the troubles of the waters on her mind. She wanted to see the preventative measure that would keep everyone from being trapped in the ocean.
The only reason she had this in mind most of all after seeing the other things was simple. Not everyone had the skills to swim and travel through the air or water. If they did, she would question the need for a ship. But the ship was their protection and safe travel. If they found themselves trapped in it, they would lose many people.