they are they same -
Using either slot by itself =
Gen5, x16 lanes from CPU No practical difference in a daily driver.
Yes, the first slot has shorter tracings back to the CPU ... chasing world records @ sub zero temps - then it might matter
Z790 Dark Manual pages 19. 26
PCIe Slot x16/x8*
Raptor Lake-S and Alder Lake-S processors have 20 PCIe lanes available for
routing. Unique to the Z790 DARK K|NGP|N, the PCIe Gen 5 lanes will be
automatically switched between the two x16 PE1 and PE2 slots.
When a single PCIe device is installed in either PE1 or PE2, the CPU will
allocate x16 PCIe Gen 5 lanes to the slot where the device is located. If PCIe
devices are installed in both x16 slots, both lanes will operate at x8/x8 speeds.
* Please see the description for Physical (length) vs Electrical (lanes) on Page 26.