In my opinion, I would think reference board designs would be a little less susceptible in terms of being D.O.A. I'm basing that off the fact that all reference boards would have came from Nvidia, still using the stock PCB.
Now, because the Nvidia boards with no other branding have not been shipped to the third party companies like you mentioned PNY or EVGA, I would imagine these boards would be viewed as the most reliable. This might justify a higher MSRP in the eyes of Nvidia.
With that being said, I have no problems not buying reference designs. In fact, I actually prefer the aesthetics from after-market coolers, or different coloured PCBs.