The BBC article wasn't clear since it was talking otherwise about new commissions, while the anniversary special was commissioned with series 7.
I'm trying to wrap my mind around the idea of a cash-strapped BBC wasting money on a 3-D television special. This news does make sense of the many oddities surrounding it -- why it's only an hour (so there's less film and less FX to deal with), why it's filming in April (long post-production time).
I have the fear that it's going to be more of a showcase for the world of Doctor Who
in 3-D (the console room, Daleks, that sort of thing) than an actual story, though.