Aaron was born at the same time Boone died. Boone could have been reincarnated into Aaron. The show's final scene, which depicts them in the church simultaneously, does not discredit the theory. Everyone appears in the church together, regardless of when they die. Perhaps the characters, Boone included, all died, go to the flash sideways, awaken, and then move on - by reincarnating. Boone died, moved on by reincarnating into Aaron, died again at an unknown time and found himself again in the church.