Port Raviel/Paisly is the only short sea route that seems to have been turned into a two-zone trip that I can see. Everywhere else, sea zones respect established sea routes. To compare, Port Raviel/Golden Farrow was made a one-zone switch, but Golden Farrow is much farther and travel between the two was always a lot more limited.
There were many things to consider in drawing up the sea zones, and not everything could be taken into account perfectly.
