When there are multiple versions of a movie, full-fledged, made-by-Plex player apps allow you to choose which version to Play. But DLNA clients will only see one instance of the movie.
If you Split Apart the movie in Plex, each file/version will be listed as a different movie, and you should be able to choose between them in a DLNA client.
Looking at the Western Digital TV Live.xml profile in Plex, I believe that eac3 will be transcoded/downmixed by Plex to ac3. Is that what happens?
If you know that eac3 is supported by your WDTV device, you could customize the device profile file in Plex. For DLNA devices this is how Plex knows which formats are supported and which must be transcoded.
This describes the process in great detail:
You would copy the Western Digital TV Live.xml to the Plex Media Server user directory, make a directory called Profiles, and put it there. Modify the appropriate DirectPlayProfiles entries to add eac3.
<DirectPlayProfiles>
...
<VideoProfile container="mkv" codec="mpeg1video,mpeg2video,mpeg4,h264,vc1" audioCodec="eac3,ac3,dca,aac,mp2,mp3,pcm" />
<VideoProfile container="mpegts" codec="mpeg1video,mpeg2video,h264,vc1" audioCodec="eac3,ac3,dca,mp2,mp3" />
<VideoProfile container="mp4,mov" codec="h264,mpeg4" audioCodec="eac3,ac3,aac,mp2,mp3" />
...
