Almost the same happened to me a couple of years ago with a thick nail. Except I had big rubber and a dh rim so there was no perforation. That is insane though... 1 in a million.
Happened during regular road ride. My theory is that this metal rod was touched with the front wheels and jumped off the road slightly. When the rear wheel approached millisecond later the rod must have been positioned perpendicular to it and went through all layers with ease. This wasn't a gentle thorn sting, it was like a screwdriver stab and immediately left me riding on completely flat tyre.
i would think if you called the rim company and explained this, they would give you a free replacement as it's so unusual, you might point out their rims are soft!! in the pics it looks like the 'rod' that penetrated the rim is made of aluminium, which is quite something, try pushing it through another part of the rim, i bet you cant!
Well, as Robby said, probably one in a million. A perfect alignment of even strongest materials can make a perfect cut I put my theory replying under 'baggyferret'