Your MKV files will almost certainly contain H.264 video. If the audio is in DTS, you'll need to convert it to AC3 (Dolby Digital), but that's covered in this thread. No video re-encoding necessary!
Your MKV files will almost certainly contain H.264 video. If the audio is in DTS, you'll need to convert it to AC3 (Dolby Digital), but that's covered in this thread. No video re-encoding necessary!
The problem with the script method is most MKV will not contain the proper audio which Apple TV requires. A lot of them will have DTS or AC3 only and you need an AAC track...as well as conversion of the DTS->AC3 if you want 5.1. Just moving the tracks from MKV to M4V will not do it.
Also I don't expect Apple will ever (officially) support MKV files.