I haven't finished yet or done the extra mission, but I doubt too little dev time was the reason it was separated. It was announced as a preorder bonus a while back, and was ready to download with the full game.I completed the mission from Jensen's Stories. Why this mission wasn't part of the main story is a mystery. I take it that the developers had no time to include the mission into the main story before the development deadline.
More likely they felt the need to have some kind of preorder bonus, so they extracted it from the main game. Devs need to get past this - I've never bought a game based on preorder bonuses.