Yeah, noticed this as well. Dome is off center even though the registration marks are fine. Interesting to note the fine marks that are there to help the machines place the "parts" in the right spot, and yet the dome is off by so much. I'd hazard a guess that the tech punched in some numbers wrong, or missed a decimal place.
I just picked my best-centered one for smo reflector.
I have to say, haven't seen a Cree with this issue, BUT also have seen many more Crees than Nichias.