I certainly wouldn't fault them for putting the story under source control/versioning or even the location they did it, but there'd be benefit in separating them into two different projects/solutions as you could essentially have a separate "engine" project that could be reused for future games and then different projects with assets/story/etc for any game that comes down the pipe.
Now, if the intent is a one off and they have no intention of drinking from the same well so to speak, go nuts.
Now, if the intent is a one off and they have no intention of drinking from the same well so to speak, go nuts.