You can set this in the Bios
on the advanced tab (Believe System Agent > PCI-e configuration ... just by head)
You can set each of the 3 M.2 Slot to PCI-e Gen 1/2/3/4 or Auto
You could off-course always use the Dimm.2 slot since the 2 drives on those will go to Gen 3 as highest supported PCI-e Generation
Edit
You also want to go into onboard devices to change PCI-e x16_1 + PCI-e x16_2 to PCI-e x16_1 + M.2_1 + M.2_2
ASUS Maximus 13 Extreme
Intel i9 11900K
Corsair Dominater Platinum RGB
Phanteks Enthoo Primo
Samsung 980 Pro 1TB
2 X Samsung 980 Pro 2TB
Corsair AX1200I
EK-Velocity D-RGB - Nickel + Plexi
EK-XTOP Revo Dual D5 PWM Serial - (incl. 2x pump)
XSPC RX480 + XSPC RS280
4 X Corsair SP120 PWM OEM Fans
2 X Noctua NF-A14 industrialPPC-2000 IP67 PWM
2 X Noctua NF-A14 PWM chromax.black.swap
2 X Noctua NF-S12A PWM chromax.black.swap
1 X Noctua NF-A15 HS-PWM chromax.black.swap