If it's not replacing SKU's, then why do it?
A lot of money went into designing the box and materials and setting up a help desk for Tech support and RMA's, etc.
I don't see it as a problem, but it's just a little strange.
I just checked the Best Buy site and they do sell EVGA, although I have never seen them for sale there. Anyway, if you were going to buy a card, saw the Nvidia branded box and EVGA, which would you buy? I know EVGA has a good warranty, so I'd go with them. The problem is, the average Joe may not know that and maybe the salesman won't offer than information.
As far as being like Apple... I mean, that unboxing was like watching an Apple product being opened, except replace white/gray with black/green.