The 9 point higher rating for eye probably pushes him over the top in terms of his overall rating...just judging by what I see on your screencaps. Pedroia's defense is stellar but Kipnis' is very good...the difference in rating there is 17 but once you get into the upper-levels, such a difference is probably fairly marginal.
As far as why a guy like him as such high ratings to begin with, I think rudel's post has that covered. I think we are all quite thrilled there will (soon) be an ability to edit players so we can make our own adjustments to the rosters!
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