Nvidia and ATI both manufacturer the main processing units for all the GPU's sold. They sell those GPU's to OEMs along with PCB designs and licensing. So yes, Nvidia and ATI do have production facilities.
Those OEM's (EVGA, XFX, ASUS, etc) must follow a basic set of rules but have some choices they can make to differentiate their products. They can increase the amount of onboard memory, they can set higher clock speeds and even design their own custom cooling systems.
So really, the EVGA board isn't going to be vastly different from any other manufacturer, but as others have said, the real determining factor is warranty length, tech support and other features. Sometimes you see some pretty good deals like offering free games or software with purchase.