reference cards do abide by NVidia's specs, and are unmodified. Lets take a look. We will look at first, the reference design for the 650 video card (just the first one that popped into mind)
This is the reference design:
http://www.geforce.com/hardware/desktop-gpus/geforce-gtx-650/specifications
Notice it has a clock speed of 1058Mhz and 1GB of VRAM.
This is EVGAs card:
http://www.evga.com/Products/Product.aspx?pn=02G-P4-2651-KR
Notice the same clock speed, but different amount of VRAM. This is not, obviously, a reference design.
This is Zotac's model:
http://www.zotacusa.com/geforce-gtx-650-zt-61001-10m.html
Notice the clock speed, it is different than the reference design by NVidia.
And EVERY manufacture is different. The "reference" designs are simply that, for reference. The manufacture will make them vary to their will. Now I have only showed you the actual specs of it, I didn't show you the code for the BIOS. I had a PNY 9800GT XLR8 edition, and I COULD NOT flash my BIOS with a EVGA brand or anything like that, it had to be the XLR8 edition, or it wouldn't work. (it was also about twice the size of the EVGA BIOS) Obviously a more complex code. Also, you can click on the product images, and see a picture of the reference card that NVidia sends their manufactures. And as you can see, no card on the market looks like that.
Also, if you pay attention, when you FIRST start your machine your video card BIOS pops up first, it will tell you the brand, and model, and the BIOS version. I almost guarantee that no other card you will see is like that. I got 2 9800GTs at the same time, and they had different BIOS revision (thus the reason I know so much about it, via extreme troubleshooting). They would not run in SLI right because the BIOS revision was WAY off...