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Gearbox did the same thing with BL2 I'm pretty sure.
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Probably so that people can buy the collectors edition later on ater they already have the game, or without having to cancel their pre-order. Not a big deal if you can get them both form the same seller.
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Don't see a problem with it really. Especially since it was done to make sure that people could play the game on release instead of having to wait for an expensive slow shipping box to be delivered to them.