This further strengthens my belief that Atris will be the final boss, DS scenario, while Nihilis will be the LS villain.
Remember all the concept pictures of Atris and Nihilis fighting? I think, at some point during the game, you'll stumble across the two in a duel, and one will finish the other, depending on the side you choose. If you are LS, Nihilis will kill Atris (or Atris will sacrifice herself for you), and vice versa. Then at the end, you'll be able to settle the score.
Kinda like the Vader/Obi-Wan battle in A New Hope.