Hello mjoelner,
Let me help you with this.
The motherboard supports PCIe 3.0 devices but as you mentioned, the processors for this chipset support up to PCIe 2.0 meaning that the cards you connect will run at PCIe 2.0.
Now If the Controller cards you connect are PCIe 3.0 it is normal that will try to run at that speed but it is important to confirm with the manufacture of those devices if are compatible with the motherboard.