You aren't planning to game on the motherboard right? The truth is mining doesn't care about pcie 2.0, 3.0 or even 4.0 so don't bother yourself with this, the only way you can see difference is when trying to play PC games which 4.0 pcie slot will perform better
Have you watched the 3.0 pcie and 4.0 pcie benchmarks in games?
The performance gain is noticeable only in synthetic tests, while in gaming tests the increase is from 1 to 10%.
But 10% is under certain conditions. I will not write links for you, you can independently find the test results in Google.
Soon, video card manufacturers are promising 5.0 pcie.