How to convert MKV to M4V for playing on Apple TV 3 with multiple audio tracks, subtitles and chapters built-in?

Here are the workarounds:

1. Prepare MKV file with H264 video track and DTS or AC3 audio track.
2. Use XMedia Recode (3.1.7.2) to remux MKV to M4V.
3. Choose "Apple TV 3 (H.264)" and "m4v" as output format in Format tab. (Remember to disable: Streaming - Fast start)
4. Choose "Copy" mode in Video tab.
5. Select source audio track (DTS) and covert to AAC (Stereo channels, 160 bitrates) and AC3 (5.1(side) channels, 640 bitrates). If the source audio track is AC3, "Copy" mode is preferred. Remember to embed 2 audio tracks in one files.
6. Find subtitles in Subscene or Shooter. Make sure the format is UTF-8 (I use Notepad++ to convert  SRT from ANSI to UTF-8).
7. Use Subtitle Edit (3.3.8) to bridge the small gaps in durations. If the time-stamp is wrong (overlap or negative gap), the subtitle will not be shown correctly in iTunes and Apple TV. Save as ASS format for later import.
8. Import multiple subtitles in Subtitle tab. Remember to assign correct "Language". Since the SRT or ASS are already in UTF-8 format, there is no need to change coding.
9. The MKV may ready contain the chapters. So leave it in Chapter tab.
10. Add job and encode.
11. Import M4V to iTunes library and add some information and poster on it.

2013/11/7 update: XMedia Recode (3.1.7.4) displays the chapters correctly with M4V format.