Because he don't trust Cheika
Cheika has shown that he will pick him in pretty much every test he is healthy and Pocock isn't available
... and some where he is available.
I don't know what reason he'd have not to trust Cheika. Cheika has clearly shown himself to be a fan of his play.
Injuries have been McMahon's biggest issue in the last couple of years. A fair chunk of his salary is dependent on playing for the Wallabies and if he can't stay fit he doesn't earn that.
Going to Japan locks that salary in regardless.
It seems like both he and his wife are keen to travel and spend some time living in another country.
Given how young McMahon is, even if he misses the 2019 RWC, he would be 29 at the 2023 RWC and theoretically in his prime.