It seems to work when scaling up the models from 10x to 100x the size. Like with my smaller ships the collision is now fixed. But things smaller are still getting offset collision.
After looking at it even more. Its no so much that the collision is offset. The collision is appearing centered at 0,0,0 and the model itself is being offset from that. The models are modeled so that the model is centered at 0,0,0 but after being inported that appear offset from that location. But the collision that is generated is centered perfectly at 0,0,0
If that makes any sense at all.