It works. I also use a software program on my computer to rotate images before uploading them.
The main problem is these software programs that display them auto-oriented for you, giving you the false impression that the image is properly aligned.
It's a situation that I have been thinking about for a long time. I've experimented with autocorrecting them on the ATP server but it's unreliable and sometimes rotates images that didn't need rotating. I expect eventually I'll get this figured out and we won't have to worry about it.