Hello, Nick,
Now that you have mkvpropedit, you don't have to look into the Matroska structure.
mkvpropedit --edit track:v1 --set projection-type=1 your.mkv
should be enough for equirectangular projection.
You can also set a default direction with projection-pose-*, as listed by mkvpropedit -l.
GUI version is available in MKVToolNix GUI's header editor: Video track - Video projection information.