I already reported this to the Cargo ships author, but they said they currently didn't have time for a fix.
Their placement code was also too convoluted for me to to make a pull request with a reasonable time investment (with knowledge of the code, a fix like that should take less than 5min, but fully understanding their placement code with all its edge cases would probably take me significantly longer than to write my own version of it).
All I could do from my side would be to add a blacklist (either hard coded, or as a setting taking a list of problematic entities/mods), but that would also prevent any quality scaling for those entities - ie. the ship would behave as if it was normal quality anyway (in this particular case, I could probably keep the storage capacity scaling, but that would require maintaining a category filtered blacklist, adding significant complexity to my code and requiring constant maintenance)...