Aight, i'll try to help you out since my setup is pretty similar, 10700k, Z490-e (bios v2201), MSI gaming x 3080
1. I don't think gpu issue is Gen4 issue because you would need a 11th gen CPU for that to actually work, 10700k only does pcie gen3, still doesn't explain your "works with riser" scenario, have you tried a different x16 PCIe slot? topmost preferable.
2. Don't think i've had any big ethernet issues, altho i force the connection to 1gig full duplex in the driver and turn off the power saving options (energy efficient ethernet + power managment tab all off), device manager shows driver version is 1.2.0.6. Did you do the NIC FW update to 1.45?
3. I've found that 2201 is fine for what i do, no huge overclocks just bumped AI OC to 4.8ghz and mesh?Uncore?ring? to max 4.5ghz