Have you tried the PCIe Generation setting in Bios?
I had issues with low/inconsistent SSD speeds and enforcing PCIe Gen. 3 fixed that completely for me.
I've just picked up a Vega 56 for 200€. If I find anything problematic I will post it here.
My old GTX 760 was running just fine on my X570 Elite.
Make sure you have the PCIe Gen. set to Gen. 3 in Bios and see if that helps.
As for the lower than expected fps..
now there's a whole lot of components and potential issues involved. I wouldn't immediately blame the board unless most other main factors have been checked on.
Is the 3900X reaching the expected boost clocks?
Is the 2080 set up correctly, so there's no power saving or fps limiting setting in place?
Is the card drawing as much power as expected?
Are the temps reasonable?
How does it perform in GPU benchmarks and are power draw and temps ok during those?