You're not going to see performance degradation from using a PCIe 2.0 connection in Dolphin. The connection is only half as fast, but not a lot of time is spent transferring data between the CPU and GPU, so doubling it won't have a large impact on your framerate.
OS: Windows 10 64 bit Professional
CPU: AMD Ryzen 5900X
RAM: 48GB
GPU: Radeon 7800 XT
CPU: AMD Ryzen 5900X
RAM: 48GB
GPU: Radeon 7800 XT