Maybe I'm missing something here... I can't find a Japan-only grading system on the Aikikai website.
You linked to the 合気会とその活動
page in your blog for what you described as one of the " two standards". However this is the page for "Aikikai Activity", not the regulations page. It contains the yearly plans and gives a brief outline of the purpose of the Aikikai.
The Japanese version of the regulations page only lists the international regulations.
Why would they only list these regulations if they don't even apply within Japan?
Also, there do
appear to be some Japanese 6th dans who do not hold the title of shihan.
Article 16 : SHIHAN
1. The Hombu examines and appoints Shihan from among persons who are 6th dan or above, and who are proficient in practice and instructing.
2.To the appointed person, a Certificate of Appointment is awarded by the Hombu.