Yes, this bird did have noticeable wear on the primaries. I think we saw this bird flying. The Murrelet had drifted behind us and when we went to the back of the boat to look for it we saw a Murrelet in flight. I couldn't be totally sure it was the same bird and I didn't get a photo of it flying. Shortly afterwards we did see two Ancient Murrelets so it is possible the flying bird wasn't the Japanese.
I don't really know why there was so much feather wear either but I think there has been considerable feather wear on some of our other rarities. Red-footed Booby and Glaucous-winged Gull come to mind.