Forgive me as I don't have the ability to test this at the moment but if I install ffmpeg and Stereoscopic, it will playback full HD 3D MKV files, with no playback issues, outputting full HD audio as well? And this can be run as an external player script from XBMC?
Hmm, I can't say for sure, because I don't keep the lossless audio, just the internal track. But certainly my receiver clicks when I pass through the DTS or Dolby track.
The only 3d bluray i keep as an ISO are ones that have a forced subtitles track (like the Avengers for example). Everything else I make a 3D MKV out of and save a bunch of space with no loss of 3D quality.
Oh some 3d blurays have the right image first instead of left, so I added a flag in the filename that XBMC calls a slightly different stereoscopic batch file that includes swapping first. See the command line parameters for stereoscopic, you can make it kick in full screen, hidden mouse cursor, and automatically exit on ending or pressing escape. Very cool for XBMC.