I think this match will depend on which Scotland turns up. If it's good Scotland -- the Scotland that just about turned over a ~20-point deficit at Twickenham earlier this year -- then they should be favourites. If average Scotland turns up it can go either way, but would probably favour Japan. If Scotland-from-the-Ireland-pool-match show up then they're done for.
Given that Scotland cannot eliminate Ireland anymore I am, personally, hoping for a Scottish win; but one that allows Japan to progress as the 2nd seed. For the entirely selfish reason that it'll give the AB's a relatively easy quarterfinal with a 99.99.....% of winning. Would also send Ireland onto France, South Africa, and Wales' side of the draw where they can all slug it out before staggering into the final.