yes, those circled areas would be from the ball, and where it would push to drive the axle forward... I'm inclined to do just as you suggest, but I'm also inclined to run it, with the knowledge that I should always pack a spare (of which I do have). Had I not taken it apart, I would have never know there might have been an issue, and I'm going to assume that is the same for many who have rebuilt and then run thousands of issue free miles...
I need to do a little more investigation to see if I flip the axle to the other side, if the balls will be pushing against the opposite side of the slot when moving forward.