Apple may in future provide support for passthrough of a DTS (dts Digital) stream. However at present only DD (Dolby Digital) and AAC streams are supported in iTunes (ATV, iOS, etc) in an mp4 or m4v container. These containers can only store two audio streams plus (x264 codec) video. The m4v container specifically can only store a DD and/or AAC stream plus video. It is important to note the mp4 on the other hand can store a DTS stream but this won't be recognised by iTunes or other Apple products. Additionally to be fully compatible with iOS (iPhone/iPad which doesn't support DD) an AAC stream should always be included as track 1 in an mp4 or m4v. If only a DD stream or (in the case of mp4) a DTS stream is included the video will not play in iTunes at all or will but with no audio present.
So this is my suggestion for anyone looking to preserve the DTS (1556 kbps) lossless track, to patiently await the day a tweak is made by Apple to just pass the signal through. Heck even if they don't you can keep the original audio and quality without conversion to DD (640 kbps). If you are on OSX there is a program in the Mac App store called MKV2M4V which will demux/remux mkv files to m4v/mp4. During the process the audio options presented will allow you to retain the DTS stream as audio track 2 (select AC3 passthrough), while creating a (320 kbps) AAC stream as track 1. This can only be done if the output file type is selected to be mp4. To include subtitles place an (identically named) srt file in the same location as the video file it is for (select and drag both files onto MKV2M4V app), and check the subtitles checkbox in the application. Also check the 'set tracks and chapters' option. Be aware this application does not transcode the video stream it just plucks (demuxes) it from the mkv container as is, which means no loss of quality from the source.
The result is an mp4 file with 1 video stream and 2 audio streams (track 1 AAC, track 2 DTS). It can be dropped onto iTunes but when played only the AAC will be visible. To play the DTS audio use VLC Media Player and select audio track 2. If VLC is configured properly and your system supports AC3 passthrough (even OSX) you will get the DTS audio stream. A helpful tip is that if you notice the DTS audio is out of sync upon skipping through the video, simply select audio track 1, then select audio track 2 again a few seconds later while the video is playing. I would warn you though the GUI is not great in the application, however it does get the job done.
If your source mkv has a DD audio stream then you can use an m4v container for output. This is an easy way to tell which files you have will have a DTS (mp4) or DD (m4v) audio stream.
The trade off for using this method is the inability to get digital passthrough when using mp4, DTS and iTunes since only the AAC is available. However the upside is preservation of the original DTS audio stream. The alternative is to use some program to convert the DTS stream to a DD stream. In this scenario you would use an m4v container with AAC (320 kbps) for track 1 and DD (640 kbps) for track 2. When added to iTunes both tracks will be available, on iOS only the AAC stream will be available (this is why it's important to include it).
Personally I chose to use mp4 to store DTS, then use VLC/Desktop/Laptop/TV for playback or suffer the 320 kbps AAC. Eventually Apple will undoubtedly elect to support DTS passthrough. With mp4 and m4v interchangeable (i.e. simply rename the file extension to change file type) when DTS support does come hopefully it is implied m4v will get support for it too.