A GTX 690 has internal 8x/8x, meaning it had PCI-E 2.0 8x and thus PCI-E 1.1 16x. Eh. I'd be surprised if an underclocked GTX 680 (effectively) would be held back all too much by that. Yes, it has a consistent and measurable effect but not a noticable one. Held back? No. But premiered by faster? Ever so slightly.
I honestly would not worry 'tall about it.