There are multiple ways to build ships that don't do this. I currently know of only 4, 3 of which were found by players, one I found because of a loophole in my configs.
Ok, i am having issues though with anything bigger than a handful of planks. If I could make a suggestion, to make the carpenters block frames have no physics and build a boat that way. Like they do in real life. Planks nailed onto a frame. Then you can allow for the bigger ships as well.
Well, hopefully Gotolink (who has taken the mod over) can resolve some of those issues so you are able to include itI've looked into Ancient Warfare, and there are many things that would have to be done on it's author's side before I could add it.