So I found that this has to do with the recent Safari update to version 10.1. My issue and screenshots are from Safari 10.1.1.
This is also reported on Physics meta SE, on mathoverflow meta, and explained in issue #1709 on the MathJax tracker.
UPDATE:
As of today (September 25th, 2017) with Safari 11.0, this issue has been fixed. All exponent symbols fall right in place. Cheers !