You shouldn't give too much credit to the idea of a coherent Nazi ideology.
One commenter put it: there was no substantial racial theory that would be official in Germany except "Jews are bad" and "Russians are natural slaves" because they are "Slavs" (the words coincide in German)
This is correct. Moreover, Hitler's confused racialism didn't seem to bend any more to expediency than it did to internal consistency. As other commenters noted, Hitler in his unwisdom considered both Chinese and Japanese to be valid races, despite the fact they were at war and he had to pick a side. Contrariwise, he said that the Indians deserved no better than British domination, despite the clear opportunity of using them to undermine the allies.
From Japan's perspective, the Germans were a means to an end. A faction which wanted to attack the Soviets was derided as 'Hitler's office boys', and defeated by the 'southern' faction which argued for an invasion of China. Japan's performance against the Soviets in border clashes had been quite poor.
To Japan, the worst thing about Britain, France and America was that they were nearby. The best thing about Germany was that they were far away.
That being said, Germany and Japan shared intelligence and cooperated to the extent possible. I remember reading on Wikipedia about an incident involving an Italian submarine that arrived in Japanese held waters after the defection of Victor Emmanuel. The crew were out of radio contact and had no idea of the cleavage between the King and Mussolini.
When they arrived, the Japanese hauled them out and made them declare either for the co-belligerent Kingdom of Italy under the control of the Allies, or the Republic of Salo declared by Mussolini. Those that declared for the king were made POWs. That they did something like this suggests they had at least some commitment to the Axis. The path of least resistance would have been just to confiscate the sub and escort all the crew out of the country.