they are indeed positional coordinate for castles and ports.
there is also orientation for ports, like which direction it sticks out from the land and thus visually connects with a sea.
I never changed those settings and it may not be that good to mess with them as the visual part may be different from that of the game engine. ie. port shows going into sea A but game engine treats it as going into sea B which can be disastrous for trade.
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