I don't even really blame Shout. If Fox had done the set, they almost definitely wouldn't have included the curtain call ending. Though I have to wonder... did Shout know the alternate ending existed? This is one of those cases I wish someone like you, who knows what they're talking about, had mentioned this to the people at Shout (on Facebook or whatever) early on after the set was announced, so they could have at least been aware of the existence of the alternate ending and then either tried to get the original version of the episode or come up with the "only materials available" excuse. Because you can never trust a company to go the extra mile for completeness without some prodding. Just ask any DC Comics fan who buys their collected editions.