I have a suspicion that Oda purposely do this to close this arc/saga. In fact, one more similarity is that the Straw Hat didn't fully use the Merry Until Logue Town, since Nami took the ship away.
So i think Oda purposely use this parallel, so that people can realize: This is yet and another turning point. the first is from searching for crewmates to Explore/adventuring. If go by the ship, then you will also notice in a majority of east blue, they use two small boats, representing they are yet a group, while prior to Enies Lobby they use going merry, good for adventuring but not much for battle.
The combination of all this show merely one important thing: One Piece is gonna focus away from pure adventuring, to more battle.