I have a feeling that he had some sort of morality system that would unlock certain things. It's the only explanation why there is like, a holy version and an unholy version of nearly identical items.
Reminds me of when I talked about my Isaac & Meat Boy Go To Hell idea, wherein the final world would differ depending on how many of a certain variety of item, like getting mostly Holy items would result in you going into the Garden of Eden to battle The Serpent, or getting mostly Unholy items would send you to Cocytus to fight Lucifer, or mostly "Meat" items leading you into Bandage Girl to prevent the Daemon Child from being born.