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No. No.
But new aTV by itself plays nothing. It needs an AirPlay streaming server. And there are ones, that do play MKV.
 
Or VLC for IOS will work too.

VLC is not recommended at all as it uses direct AirPlay, meaning horrendous image quality / framerate.

If you do want to play back MKV's from an iOS device without remuxing and over AirPlay, currently the only one way to go is Infuse. (The iOS6-compliant 1.5.x will do, you won't necessarily need v2, which is iOS7-only.)

See my additional posts at https://forums.macrumors.com/threads/1680468/ for more info, where I've explained this all. (I'll also publish a full review of the player some time.)
 
Best way is to remux with Subler to mp4 format and play with itunes via airplay.

Exactly. Only the native mode of AirPlay should be used, which can only be done via iOS-native media files (mp4 / m4v / mov) or Infuse's MKV / MTS support.
 
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