Yes, the graphics card does not fully use up the pci-1 1.0/1.1 x16 slot bandwidth, even though PCI-E 2.0 slot has twice the bandwidth, since it doesnt use up all of PCI-E 1.0/1.1, then its not going to use up PCI-E 2.0s bandwidth.
I guess an nice example would be you having an car that can go 80MPH (graphics card), and you are on a freeway that lets you go 100MPH (PCI-E 1.0/1.1), then you decided to go on the freeway that lets you go at 200MPH instead (PCI-E 2.0), but you cant go that fast since your car can only go 80MPH.
The only difference you will see are in benchmarks, while in gaming, there was no difference IIRC.