I don't understand anything you're talking about but I'm glad you found a good solution for your audio playback 
But, ... it can.Me neither. The title suggested hi Res audio through the ATV but it can’t do it so I’m a bit confused by the thread (avoiding the debate about hi Res audio)
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Brian, thanks for sharing this piece of good news!... Basically for me the ATV4K does everything I need so I was happy to find an easy way to have it do this also.
I was in the habit of making my High Res Audio into Flac files which are nice but when it comes to surround sound I have only a handful of albums that I prefer to listen to as complete albums. (Chapters still can make it easy to que up a particular song.) ...
I will have to test... I don't see any reason why Plex would do something wrong with the multi channel FLAC files. I know it can play them. I will go check now. This will be fun.Brian, thanks for sharing this piece of good news!
So must they be MKV's, or can you play a multichannel FLAC in Plex?
I also have JRiver MC 24, and it runs on a dedicated HTPC in my main Theater and feeds my preamp via HDMI, but I also have a secondary Media Room with an ATV 4K and would love to play some of my multichannel music there as well.
Most of my DVD-A and SACD rips are in multichannel FLAC, as individual song files withing album folders.
Only a few recent music BluRays are in full BR disc file format, which I assume Plex can handle and send the bitstream via MAT to the receiver (so as to preserve true high-res and Atmos), is that a correct assumption?