The difference was the Twilight Sparkle Blind Bag that came with it. It turns out she got wings so it's a completely different mold! Hopefully they will continue using this mold for her in the regular Blind Bag waves. I think it looks really cool!
You can order it on the TRU Website for $15.29 during the current sale. The Regular price is $16.99. Ignore the box art as it's an prototype with images from a Rarity Brushable Custom. However, keep in mind that we don't know yet if people will receive the second release or the first one. It has also been listed on Amazon here and it seems like there are even MORE versions of this game by reading the comments. Some of them come with cardboard Ponies so the best is to inform first which version they are selling!
Many thanks to Ryan for the heads-up and images!