The game has a limited number of harbor/city objects. They are dropped on the map as a big blob. This obviously limits choices. Presumably it's possible to take them apart and make more complex arrangements, but it would require a substantial amount of 3D skill, not to mention all the hex stuff to get them opened and back together.
FWIW, the mission editor is actually prettty straightforward in terms of using the stuff already available if you want to give it a try. Also, it has a "merge" ability so you can practice on a blank slate, and add it to the game file once you have it worked out.
tater
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