Sorry but the cpu has nothing to do with Pci-express 2.0, its the board that handles all of that.
With the chip set on the motherboard.
North and South bridge chips on the motherboard,handle the Pci-e express slot, be it 2.0 standard or 3.0 standard. And all the other expansion ports or devices you are able to connect to the motherboard. Not the Cpu.
Your confusing the fact that the Cpu also, has an Intel HD 4000, or 3000 graphics solution on the same Die stating it will run at Pci-e 2.0 spec. However the board states it will run a Pci-e 3.0 graphics card in the Pci-e card slot. since you are not using the in built graphics solution Incorporated as part of the Cpu. you will switch that option off in the bios and select the Pci-e graphics slot of the board with the card in as your default primary output display to the monitor.
So there is no problem at all, it will work. 3.0 graphics card in the 3.0 spec Pci-e card slot of the motherboard. There is no problem vaggospro.
It will be good to go, I hope this has helped you to understand how it all works anyway.
vaggospro. Good luck.