Oho! Yes, I suppose once one has gotten past you-know-what it is likely enough one would consider you-know-what to be a finished task, and so miss the item. But I suppose some other gamers would have an instinct of looting foes, and so would do fine, haha.
Unless you mean the note after the "small dark thing that requires some kind of food" leaves - the puzzle of that note really is the "final boss" of the game so to speak.