sate slotThe second M.2 slot usually does run through the chipset, which is also where the SATA controller for ports >5 usually does reside. And sometimes yes using the lower M.2 will disableSo a gen4 drive in the 3.0SATA slot will be limited to gen3 speeds, as will a gen3 drive in the 4.0 slot. But either will work just fine. So if you get one 3.0 drive, mht as well put it in