Travel in the Second Ether, due to it's nature as the origin of raw Chaos, alters organic and inorganic matter alike and those who frequently use Scale Ships are heavily altered from exposure to raw Chaos energy. A mechanical object in the Ether will gradually become organic, and vice versa. Each ship has a "Main Type", a captain of sorts who becomes one with the ship and acts as it's ego. The entire crew will sometimes be one with the ship, as in the case of the Spammer Gain and as observed briefly of Billy-Bob Begg's crew, and are indistinguishable from the ship. In these cases, the ship and the crew combine to create a virtually new lifeform.
Scale Ships are utilized by the Chaos Engineers, The Singularity, and other multiversal travelers. The Meat Boats of the Machinoix are most likely Scale Ships, which explains their techno-organic nature as well as their ability to enter and exit the Biloxi Fault unscathed. It is also quite possible that the Dark Ship is essentially a Scale Ship, since it sails the "seas of fate" between worlds.