Quote from Iwata Asks interview regarding New Super Mario Bros. Wii: Given what Miyamoto said, and the context of that screen-shot. I'd like to think that Super Mario DD screen with Mario and Luigi together is the real deal.
I bet Rare had just one engine for N64 that they just tweaked over and over again for Banjo Kazooie, Donkey Kong, and Conker (both incarnations) They all seem extremely similar in gameplay, nature of collectibles, audio, and scenery...
Jimmy130 point me out to this article: http://www.gamekult.com/blog/jimmy130/140243/Super+Mario+64+sur+64DD.html