If, and this is still a rumor, they come out with two devices for the next gen Xbox, one the Xbox tv and the other the full gaming console then we could see more formats and containers supported. Or, and I expect this to happen, they extend the apis from windows and windows phone over to the next Xbox and offer a real app store. If that happens then the same media players that we see so far for windows 8 and RT can also find their way on the xbox. At that point we can get 3rd part apps that will play mkv and flac and whatever else you can want.
Even if Microsoft offers an Xbox TV device it will want users to buy approved content and to maintain its relationship with media producers, so it's unlikely that Microsoft will support MKV or FLAC. This isn't an accidental policy based on a lack of resources.