If the HTPC doesn't have to do it in real time, ie the stream is decoded before the movie is played, the problem is much simpler.I think the only hope for HTPC decoding of Atmos is if Trinnov licenses their custom decoder to someone like JRiver. Their ultra expensive pre-pros are i7 based custom built computers, so I'd venture to guess the decoder is software based.
The "easy" way to do this is to set up an atmos receiver, connect ADCs to every speaker channel, gather a bunch of data and then compare what comes out with what comes in. One should be able to find the pattern.
I suspect that the track has base, channel driven sounds and then a couple(variable number) of object sound tracks where the object track has a moving location within the soundfield.
If one compares the True HD track to the atmos track, one should be able to isolate the moving object tracks.
This would be a very challenging and fun project to work on.