The example playercorefactory.xml file will cause both .m4a and .mka audio files to played using the Videoplayer, as opposed to the PAPlayer of Kodi, normally used to play audio files.
Having your audio tracks as MKV or MKA files should invoke the Videoplayer in both cases.
Its the PAPlayer of Kodi that is not indexing the the last of your MKA audio tracks, which I assume were in a single folder.
With your audio tracks in a single MKV file, it is possible to add chapter names using MKVToolnix. You can use a text file with a specific format to define the chapter timestamps and names, then use MKVToolnix to merge it into your MKV file.
Alternatively, you can use Handbreak (HandBrake Documentation — Chapter Markers) to automatically generate chapter markers and rename them, or import/export chapter lists from CSV files.
It’s the PAPlayer of Kodi that is at fault.
Have a look at Dolby Atmos for music - #33 by thechrisgregory for even more analysis/explanation.