Wasn't the Twin Peaks situation a rights issue? I don't watch the show, so that may be inaccurate. At any rate, I don't see a scenario where the QL pilot is left off. Fewer people have the out-of-print pilot disc than not, I would imagine, and leaving it off would probably lose a few customers and knock the episode count down to 7 episodes. Maybe the Battlestar situation is instructive, as Universal released the movie version of the pilot long ago and included it in its original format in the current box. They also made the movie version available separately, I believe.