Unfortunately there are still some problems.
1) Now that the video stream is included, JRiver is tagging the files are video instead of audio.
2) Most of the tags that were added with MP3Tag have been lost. The album artist and genre remain but the album title and year have been cleared. The files end up in a new folder called "Unassigned" in my artist folder, instead of assigned to a folder with the album name.
3) The JPEG embedded in the file has been lost as well so there is no album artwork. If I play a track as a Media File, then the video stream is displayed along with the audio. If I play a track from the Unassigned folder (as music) then just the audio plays and the screen remains blank.
1) can force MC to classify this as audio (Media Type)
2) once it’s classified as audio can repopulate tags
3) can embed cover art using MKVToolnix that you already using
But what bothers me ... if you just choose “TrueHD Atmos” in MKVToolnix ... result should be mka ... bitstreaming that to your receiver should trigger Atmos ... can you MediaInfo mka to see if MKVToolnix correctly remux Atmos track
EDIT: also when you play mka to your receiver ... does it at least show TrueHD ... if not, you might not be bitstreaming and applying some DSP for audio only ... ATMOS metadata get lost in DSP
EDIT2: you mention that when playing mka ... your receiver displays Neural-X ... that’s DTS feature ... you might have ripped DTS track first time instead of TrueHD Atmos