How should the castle be positioned to allow access to the shipyard?

How can that be? Can't you define those circled x and y? And click to the right of them? Or all the way to the right of them? The symbol there should indicate that they are clickable.
You can open the map with an archiver, find the map.xdb file with Notepad, find the city in it, and change the desired properties manually, without using the editor (close the editor beforehand).