I renewed my NZ passport recently, using a photo taken on my wife's phone, and after seeing the stuff headline, I thought it might be an idea to relate my experience.
The photo was rejected as having the wrong orientation. It looked fine on several phones and with several ways to view it on a computer.
Then I stripped the metadata (using imagemagick), and then it showed sideways in viewers. I could then rotate it upright, and they accepted the rotated photo.



