In addition to Anssi Hannula's response on the ffmpeg mailing list I found two alternative methods for extracting the DTS core from a DTS-HD MA that are linux friendly.
tsMuxeR
Available from the Doom9 forum. Can be ran via command line using a .metafile, which itself can be generated from the tsMuxerGUIor you can use the GUI directly.
Application is 32 bit which can make it tricky to install on 64 bit systems. Alternatively, you can lesser the burden by using third party repositories e.g. for Debian try deb-multimedia.org
MakeMKV
Can be compiled for Linux (e.g. debian based systems) using the instructions on the MakeMKV forum. Run MakeMKV, select the source .mkvfile and then just select the DTS core audio stream. You cannot deselect the video stream.
ffmpeg vs. tsMuxeR vs. MakeMKV
ffmpeg was quickest on my Debian box, followed by tsMuxer and then MakeMKV. The latter required you to copy a video stream in addition to the audio. The resultant output is an .mkv file that contains a video stream and the DTS core audio.
Both ffmpeg and the MakeMKV approach seemed to produce the same bit perfect output files, whereas tsMuxer was marginally different as shown by file sizes and md5 hashes:
MakeMKV approach 1103097108 7b0c0fb9f8db27e9bf7aef351eb4fbda
tsMuxer_approach 1103097236 021552f6ae4387b15635f9d0f0a9d7f0
ffmpeg_approach 1103097108 7b0c0fb9f8db27e9bf7aef351eb4fbda
So in summary, Anssi Hanula's method using ffmpeg is the most effective.
Relevant FFmpeg bug report: #1920 dts-hd core extraction.
– llogan – 2014-09-19T18:18:58.870