The little kitty now on your bed has evolved from cats that lived in the desert. "Whether or not your cat decides to dig a hole to hide their urine and feaces before or after they go will depend on the cat, but this behaviour is generally a mark of their territory," notes Dr. Miller. For example, if your cat's litter box is located where he doesn't spend most of his time, he would probably consider that his peripheral territory, and that will affect whether or not he decides to cover his feaces.
Smell is a very important factor for cats to define their own space. If your cat considers his litter box to be outside of his normal "territory," he might not cover the remains, as advertisement he still considers that area his. If it's inside his territory, he might be more inclined to cover up the smell, since generally cats are pretty clean creatures.