Could someone justify (or explain) how Japan remains a Chicago Convention signatory, while they clearly disagrees with the principles of Annex 13 (I know about the deviations, but they seem to have even the fundamentals of accident investigation "wrong" from the Western point of view)?
No need for the reader to justify or explain.
You made the allegations without citing support for them. So perhaps it is you that need to justify your specific complaint.
The investigation is a separate entity from a justice system. Just about the same all over the world. You may be critical of their justice system, but I doubt they care.
However if you meant to be critical of their investigation then you seem to have left out supporting reasons.