It seems the blu-ray box set only will include all the special feautures. DVD box set will have just the deleted scenes.
Blu-ray Special Features:
- The Arc of the Story: Mining the Human Emotion: Cast member and writers and actors recalls Season 2 highlights
- A Visual Masterpiece for the Small Screen: How the Visual Effects Artists Push the Envelope on an Ongoing Basis.
- Detached Memories: Unaired scenes for every episodes.
- Bloopers Reel