It looks like an unreliable modification. Running a GHz-level interface with jumpers is almost impossible to control the impedance, it's a cool Proof-of-Concept though. But is it possible to bring the project to the next level? Is it possible to make a daughterboard with QFN connector? If so, one can make a pin-compatible daughterboard with an extension connector. To use it, just desolder the USB chip and solder a ne…
That said, PCIe phy’s are extremely robust - they do most of the impedance matching and delay mismatch training. And if you don’t ruin the onboard caps, this could be jumpered straight across.