At the end of the war, Merrix wanted to experiment with ships in the style of elemental-binding without having to rely on Lyrandar or Zilargo. So maybe he used a lot of Khyber shards to attune the ship directly to the plane of Mabar and have the ship channel shadows without actually binding elementals. Now controlling the ship would be a lot more complicated, which is why they created Shade to be the pilot. Also, the ship probably starts sapping the life out of everyone on board which made them cancel the project, but warforged are immune to that effect.
More on the warforged known as Shade:
When Cannith South started experimenting with different kinds of airships towards the end of the Last War, Merrix decided to head a project to create a shadow ship, connected to the plane of Shadow and capable of traveling with an effect similar to the shadow walk spell. However, the artificers soon discovered that they weren't able to control the shadow elementals/energies in the way a heir of Lyrandar could control a bound elemental, and instead they went to work create a special kind of intermediary. Out of this desire, Shade was created. A warforged imbued with the essence of Shadow, it was constructed to complete the shadow vessel House Cannith wanted to perfect.
Gurv helped me with the idea behind how it works because he is awesome:
I would maintain the shadow ship's status as a plot device instead of clearly defining it...
Here is what I would do. Merrix didn't have Zil elemental binding technology. He did have advanced warforged technology. So he tried to substitute one for the other, with mixed results. Shade is essentially a very localized manifest zone to Mabar, constructed with khybershards and the like. Instead of a Wheel of Wind and Water, the helm of the shadow ship functions more like an attached warforged component (I'm picturing heavy wires and cable running to his docent slot as well as to points all over his body). When linked to the ship, the manifest zone encompasses both him and the entire ship.
When the shadow ship is functioning, it opens an energy rift to Mabar. But it doesn't pass through it. Instead it shapes the rift into a ring that provides propulsion. At the same time the negative energy makes the whole ship (plus occupants) insubstantial and shadowy. The drawback is this: while Shade is immune to energy drain as it applies to humans, the longer he keeps the rift open the further he is drawn into Mabar. After a while it becomes a constant effort not to slide over entirely. Should that happen, it's too bad, because its a one way trip (I actually see the rift as causing a flow of energy towards Mabar).
That gives you a measure of control over things, as you can determine how far Shade can go without dooming everyone. The other brilliant idea I have is that Mabar is the Endless Night. If the shadow ship is powerful by a rift to that plane, then it simply shouldn't work during the day. The ship should be dead in the water, like a normal airship with its elemental suppressed. It might be able to move a little with mundane sails, but that isn't really part of the design ad it raises the initial problem of being knocked out of the sky. At night the ship is fast, insubstantial, and almost invisible. During the day, it becomes a sitting duck.
I hope that helps.