That charging cradle/stand will work through two contacts under the controller. You can see the contacts on the charger marked 213a and 213b. Exact same way as how the 3DS charging cradle works (as well as many other charging cradle things).
So the port here isn't for this. It could be used to charge + play at the same time via a wire (think about the 3DS again with how it uses its charging port to charge with the wire, but not when using the charging cradle), but I'm betting even if it could do that (I have my doubts unfortunately, but at least if you can't play + charge at the same time its battery should last long enough to play as much as you want in one go, otherwise nintendo will end up with people complaining all the time that they can't even use the new controller, which would be a huge problem obviously, something I doubt someone like nintendo would overlook). I'd say it's more for extensions, like how the wii controller works (remember that wii U zapper we've seen)