Yes because Mystery Dungeon games often take place within the same world as the main series Pokéon games, and all spin-off games take great care to place themselves within the established canon of Game Freak's works.
Anyway, Chunsoft haven't been doing that much lately - they pumped out Shiren 4 and 5 last year and released some random DS game early this year but there's not been much since, and there's been no Pokémon Mystery Dungeon for a while - so it wouldn't be a surprise to see that they've been working with the 3DS tech for a while, or working on what they did for the Wiiware Mystery Dungeon games.