Thanks to Pascal Dornier of pc-engines who pointed me to the BIOS and Kernel Developer Guide available at https://www.amd.com/system/fil…h_Models_30h-3Fh_BKDG.pdf and specifically to the USB section of it, I could identify what needed to be done to re-route the physical USB-A connectors on the APU2 from XHCI to EHCI:
* re-route the USB8+USB9 from XHCI to EHCI
* enable the EHCI2 controller
* re-xcan the PCI bus to detect the new EHCI controller
Afterwards, any devices plugged into the USB A connectors on the APU2 boards enumerate on the EHCI instead of the XHCI controller.
The source-code of a related tool to perform these steps is available at https://git.sysmocom.de/sysmocom - in case anyone else runs into this problem.