The Magic-Con deck is absolutely a D&D deck. Magic-Con is their brainchild, and they are very hands-on with every element of the convention.
The first Magic-Con did not have a dedicated deck. Attendees were given some early S&M decks, and the v4 was first introduced for sale there.
The first MC deck was available at the 2nd Magic-Con in 2011. Genii was a sponsor, but this was still D&D's convention, and the art, print run, etc, was all done by them and their team.
I'd imagine they will have a 2nd MC deck at the upcoming 3rd Magic-Con.