MKV is a free and therefore very common container format. It can be played with software players (e.g. MPC-HC or Power-DVD). But also many (UHD) BD players or smart TVs can play the format via network or from a USB stick.
Since this format can accommodate all conceivable codecs in itself, this case will probably include an E-AC-3 JOC or MPL with Atmos file.
A really very interesting concept to bring Atmos to the people. 
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MKV worked perfectly to me.
Was using it to “package” mlp (TrueHD from DEE) or mp4 files (DD+ from DEE or DAPS). The mkv-files play fine on an Oppo BR-Player connected via HDMI to an Atmos-capable AVR.
Am using ffmpeg to package the files coming mlp or mp4 files coming from the encoder. FFMPEG is free and can be downloaded from many locations. Here is the command for Windows command line.
ffmpeg -i file.mlp -c copy file.mkv # the copy flag leaves the audio un-touched.
With some more effort put into FFMPEG, it is even possible to have multiple audio-tracks in parallel with a MKV-file. E.g. Stereo, 7.1, Atmos-DD+, Atmos-TrueHD etc. The tracks can be switched in (most) soft-players and also the Oppo hardware player.
While digging through all these things, I figured out, that MacBooks do not support Bitstream Output via HDMI.
This is a disadvantage in that you can’t play back your Atmos-Audio to an AVR. With Windows-PC this does work.
LG, Juergi
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Thanks for sharing that info, Juergi!
I would also like to recommend the free program MKVToolNix. This is the de facto standard when it comes to creating MKV files. It has a clear GUI and you can easily drag almost any format (even other container formats) into the program. So you can create MKV files with many audio tracks within a few minutes. (Of course also tracks with Atmos.)