Just because he's not old fashioned doesn't mean that he's always right.
I'm on board with Cora. He's done a great job, so in no way am I trying to knock him. Besides, whether JD bats 3rd or 4th makes so little difference over the course of the season (2 runs) that it really doesn't matter.
All that said, if you want to optimize your lineup, you do not put your best hitter in the 3rd spot.
Also, while I'm on the top of JD, he still stinks defensively. The only reason that I have not brought it up lately is because there's really no sense in arguing about it. It's not because he's actually good out there.