Some parts line up better than others! There is a great deal of asymmetry in the ship, mostly in the longitudinal alignment of features. The gunports are actually pretty even in size on each deck, but they do not align side to side. As you suspected the masts are not exactly on the hull centerline, since it is difficult to define a single centerline. The masts are more or less in the center of the deck, but the deck is not centered over the keel, so the mast steps are offset slightly to one side. The masts are also not exactly in line with each other. Much of this is the kind of detail you would find in any wooden ship if you could see it complete and looked closely enough, but some aspects of Vasa are especially odd, like the misalignment of the gunports.