The Vault is an isolated dimension which has no bearings on the real world which is why Atheon, The Templar and Gorgons are not seen anywhere but inside of it. If they could succeed in transferring their existence into the physics of our universe we would cease to exist. Once you travel into this dimension however you can be erased from time (as Kabr and his team were) which is why they are/should be referenced as they have/had bearings in reality.

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.