For JRiver, we're on a quest to find a method to:
1. Get Atmos BDA tracks into the JRiver Audio Library
2. Ensure gapless playback for Atmos tracks in River Audio Library
3. (not critical but ideal) Have individual Audio files (allows adding any song to a playlist)
JRiver has a feature called "Particles".
Particles - JRiverWiki
In this example, I created one MKV with all the songs, and all the audio streams (Stereo, DTS-HD 5.1, Atmos).
I added the MKV to JRiver -- it shows under the Audio library together with all the other audio files (FLAC, SACD ISO, etc).
I added 3 "particles" (i.e. 3 individual songs) -- each particle is just a reference/pointer within the MKV (with a start / end time).
In the screenshot below, the first 3 lines are the particles, and the last line is the original MKV. If you want the Particles and the whole MKV album to appear as separate albums, then just use a different album name for the particles and the whole MKV.
So if I play the "Here Comes The Sun" particle / song, then it goes to that part of the MKV.
As I mentioned, the MKV contains all the audio streams, so I'm able to select any of the streams, including Atmos (which will stream properly to the HDMI / receiver as Atmos). I believe you mentioned that Atmos only works in JRIiver if it's the only audio stream in the MKV -- but that is not the case based on my experience.
JRiver 'remembers' which audio stream you selected the last time you played each individual particle/song. So if you selected Atmos the last time you played that song, it will select Atmos the next time you play that song, even after you restart Windows. The same thing applies if you play the whole MKV.
Each individual particle / song can be added to a playlist, together with other file types (FLAC, individual song within a SACD ISO, etc).
When you play the particles, there's a pause and it's not gapless when it plays the next particle.
If I want to play the songs gapless, then I can just play the MKV itself (not the particles within the MKV). so of course the MKV will just play continuously.
Or if you have a couple of favorite songs that you want to play gapless and add to a playlist, then you create one "Particle" which contains those two songs, then add it to the playlist.
Edit:
The particles feature also works with the Blu Ray BDMV disc folder structure / backup.
And you can also add those particles/songs to a playlist.