I have another theory. The factory stamping (or forming?) machine had a hiccup and the brass around that punch (or shape-former?) snagged on on the punch (shape former?) and following the punch down, and then back up when it is retracted, weakenning the brass in a larger circle but leaving the crumpled brass in a circular pile. The primer just blew out the weakend protion of the circle. This may be why you saw it to be normal when you reloaded. Also, it may explain the increased scorching in the primer pocket. The crumpled (creased) circle of brass may also have not been level, thereby keeping the primer up a fraction more than a properly seated primer. That is why you do not see the "shadow" of the anvil because there was too much room between the rest of the anvil and the remaining base of the pocket. It is possible (?) that the crumpled brass circle was touching the center of the anvil because it was crumpled up at that point and this is how the anvil had something to be pushed againnst. Too bad you don't have pictures of the used primer as well.
The fact that your other cases have rough tool marks, cratering and bending, on the other cases leads me to beleive that this theory is a possibility
Just a wild guess.