Why are the port arrangements in Better Settlers not like the arrangements in my game?
I created Better Settlers and the other answers are correct in that the version that I usually play with, the harbors are completely individualized on their own hexes so it's possible to completely randomize them. Newer versions of the game have the continuous puzzle-interlocking pieces to make things quicker for setting up.

The reason I chose not to force harbors positions even after the new version is I found that it was possible to create better and more variable board setups if I didn't add the constraint of fixed harbors.

The best solution with new versions is to flip the frame pieces over (so harbors aren't visible) and then use the additional harbor pieces that come included with the game (you can even just use a piece of paper if you don't have the additional pieces).

Hope that helps!