Actually, now a days, it's not both versions. It's usually one version of the film and the extra scenes.
For example, the Lion King DVD had a new extended cut that was only one scene. Essentially, the first disc had the theatrical cut of the film and when the new part was suppose to come up, the new scene seamlessly integrated into the film without pauses. You couldn't tell that the branching was going on. It was the same with the new Gladiator Extended Cut DVD. It's the same with the new Passion of the Christ DVD. It won't be anything like what we got with the first X-Men DVD.
DVD technology is way pass that now. Again, more than likely, you won't be able to tell a difference....unless the new scenes aren't color timed to match the theatrical version, ie X-Men. But, I don't see that happening.