There are similar bug reports for the FW16 AMD. E.g. the DEG2 over usb4 / thunderbolt works on windows, but not on linux.
All the AMD pcie low level programming docs are under NDA, so impossible to make progress on by you or me. Progress is only possible if AMD spend the time on the problem.
In short, it appears that usb4 / thunderbolt pcie link training and redriver control works differently in linux than windows.
Regarding usb4 / thunderbolt vs oculink.
Oculink has lower latency. So usb4 vs oculink 4i apparently sees noticable improvements for games. Going to oculink 8i vs 4i is apparently hardly noticable.