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.
If you look at the Japanese page they have a link for the International Regulations with a link for the Domestic Regulations below that.
On the Domestic page they have the rules for the recognition of organizations, but not for fukushidoin/shidoin/shihan.
It doesn't contain the fukushidoin/shidoin/shihan regulations - because there are none, really, for Japan.
Anyone 6th dan and above and instructing in Japan can be called a shihan, and no special certifications are issued - as per Mr. Tani's clarification.
The title doesn't really mean much in Japan - but it doesn't mean much abroad with the special certificate either, so why create this convoluted double standard?