Enchanted Golden Apple was included in dungeon chests as a very rare item with only 0.7 % spawning chance. That apple was swapped by the one crafted with gold nuggets but not changed back when the Enchanted Golden Apple was reintroduced, despite Dinnerbone's interest in inproving dungeon loot.

The odds of finding an enchanted apple in a dungeon chest is so low, that the right reward seems to be the Enchanted Golden Apple.