You're not losing any performance if that's what you're worried about, both because neither GPU is bottlenecked at PCIe 2.0 x8 (equal to PCIe 1.0 x16), and because your CPU is not fast enough to unleash your GPU's full capabilities in some CPU heavy games.
Does Radeon Settings backup your reading? And also did you perform a clean driver install using DDU between your nVidia and AMD card installations? Clean Install AMD Graphics Drivers
As you can see, my current bus setting is indeed only PCie x16 even while running Furmark. That indicates v. 1.x
So that agrees with all the other apps I've tried.
And I can say that based on testing TechPowerUp did with a GTX 1080 which is in an entirely different league than the RX 590, faster by well over 50%, and even at that level PCIe 1.1 x16 yielded 94% of the performance that a fully unrestricted interface (PCIe 3.0 x8/x16), which means a card which is half as fast is not in any way restricted in performance at PCIe 1.x x16. Your CPU, which is extremely slow by today's standards, only 75% as fast as the low end R5 3400G and half as fast as the upper mid range R7 3700X, is a much larger hindrance to performance.
