This is pretty normal - the BBC doesn't make its own TV anymore, it buys it from production companies, like Bad Wolf, and as the BBC still owns DW and trademarks etc. they'll still have control as they have done (probably for worse, unfortunately, at the moment). I hadn't really looked to see who's been doing DW for them lately but maybe BBC Wales counts as a separate production company?

(TV Centre and all its in-house departments are all long-gone, have all been dropping off for about 20 years and more now. Like, a lot of early 2000-2010 BBC productions were made by Kudos - Spooks, Hustle, Life on Mars etc, which also made some things for ITV and that's how everything's done these days, pretty much.)