Atheon and our actions in the Vault of Glass are not included in the timeline because they haven't had any tangible effects on the story of Destiny. For example, opening the array has lead to some interesting additions to the Rasputin Grimoire, and a follow-up mission in The Dark Bellow. For now, in the world of Destiny, Atheon is still alive after every Tuesday, as is Crota, and that is why his and Crota's death is not a timeline event.