Japanese have been sedentary farmers for 2000 years and been writing Chinese Buddhist and Confucian works for 1000 years. If a Chinese scholar of 1640s is offered a choice of a Manchu employer or a Japanese one, who'd he prefer? Would Japanese demand that Chinese cut their hair?
Japanese were already sinicized to an extent the Manchu were not.
First, there is no garuntee that Manchuria would rise to conquer China and contest it with our hypothetical Japanese conquest of China. Because butterflies.
Second, Manchuria has, as of 1640 an 800 year period of scinicization under the (arguably only half Manchu) Liao and Jin dynasties. That is not much behind Japan.
Third, is Japan really that similar to Ming China? Does Japan place a focus on bureaucracy? No. Japan places a focus on its warrior culture far more than the Manchus do, so much so that by the 1600s, samurai were already on their way to becoming the administrative branch of the Japanese government. Will the Manchus replace the Chinese beauraucracy with a warrior class? As history has proven to us twice, they will preserve the local Confucian beauraucracy.
Finally, given the Han psyche of the time, choosing between Japan and Manchuria would be like choosing between a hanging and a beheading. The anwser is simple--you serve the local Han warlord until the warlord is defeated. Then you surrender to whoever who has conquered the province.
No one will and no one has conquered China without scinicizing. Japan of the 1600s has not scinicized enough.