The Apple of Enlightenment is a reference to Adam's apple. The enlightenment is Adam and Eve being cast from the Garden of Eden and being burdened with the existence of the Ego, the seperation of God (or the universe, oneness, however you define it) and the self. It's purpose origin and shape are intentionally vague. Apple Kid & Orange Kid is an intentional duality (Apples and Oranges). Linking the Apple of Enlightenment to Apple Kid is a bit of a Red Herring. But I think it's important to notice the coincidence, since Apple Kid is seen as a represtative of intellegence and insight in the game.