I can't help but find a rules package for each Chaos God somewhat unimaginative. We're got a whole expanded universe to play with free from balance concerns. Here's some of my ideas for special components to that end -
Sirensong Emitter - Attached to the main vox masts, the Sirensong Emitter contains the essence of a trapped Daemonette. Enemy ships find thier vox frequencies bombarded with a cacophany of hell-spawned screeching, lasvicious moans and other soul-rending sounds.
Divine Chamber of Farsight - A rune-inscribed chamber below the ships bridge, the ship's sorcerers gather here to perform vile rituals to bargain hidden information from the Warp.
Machine-code Contagion - Enemy ships that open insecure comm-links and noospheric complexes are prone to infection from Warp-born Machine Spirit degredation broadcast from what used to be the ship's medical decks. The machine-spirits of infected cogitators rapidly rebel and decay, effectively shutting down the enemy from within