Sorry for not reading your post well enough. You could make the coastal clearing a part of the river port complex, however then you wouldn't be able to create ports anywhere except where there are rivers (or make it possible to make river ports everywhere coastal). This is obviously not desirable.
I don't think we will revisit the port mechanics for EB1, but you could create a minimod if you can think of a way around this problem and would like to implement it.
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