I've so far only tested this with boats (I haven't researched full cargo ships yet), but it appears that the boat still collides with custom fish that may be introduced with other mods.
In my case these are the fish are labeled as being part of Space Exploration and Angel's BioProcessing.
Edit: I just confirmed these fish are introduced by Angel's BioProcessing
They appear in the game as "Dorflup Jellyfish," "Levac Fish", and "Santa Ray"
