Haha. I saw that tweet and got a little excited. I can't help myself.
Batting order does not make that much of a difference, unless a manager is going to truly optimize his line up by bucking all tradition. The difference between JD batting 3rd versus batting 4th amounts to 2 runs, on average, over an entire season. I completely agree that batters should be placed where they feel most comfortable. If JD has expressed a preference to bat 3rd rather than 4th, than by all means, Cora should leave him there.
All that said, I am a firm believer that your best hitter should not be batting 3rd, and I will continue to make that point. IMO, JD would be comfortable hitting in either spot, and over the long run, the team would be better off.