As for the "empty" Storage Crates. They are not empty. All storage from all sources is automatically combined into a single accessible inventory. You can only access this inventory from Chests. I admit is was painful to watch you check every chest in the camp not noticing they all contained the same items.
lol I feel kind of silly, but I was sort of overwhelmed by how many pawns I had and how much they were doing on their own. Also it 'felt' like the containers were different because they are accessed independently and I was instructed to build multiple ones in different places.