I don't think we can underestimate how important for her to be able to qualify here, rather than at the National's. The Japan has large and deep pool of talents, and even though Miki has been among the top skaters, anything could happen at the Nationals. Why risk it?
Also Miki trains in the States, meaning she would have to make another long flight to Japan in a couple of weeks (Japan National is from 26th to 28th of December. My folks still live in Japan, so I travel frequently between the States and Japan. It means you would have to spend more than 20 hours of flight/travel hours with anywhere between 11 hours to 14 hours time difference. Believe me, it does take toll on you even though you are as young and fit as Miki, especially if you also take into account the added stress and risking exposure to seasonal germs.
I agree it was a cautious skating, and I would have liked to have seen more aggressive skating she was capable. Still, the prospect of her performance at the Olys warms my heart.