Using “bitbake Linux-toradex -c menuconfig” I remove the “bus support/PCI” feature, rebuild and update the kernel (and kernel modules) in the Apalis evaluation board and then my USB devices stop working i.e. not detected at all. Does this mean the PCI and USB h/w are somehow “tied” together on the Apalis evaluation board?
I guess you are using an Evaluation Board. On this board the signal RESET_MOCI# resets the USB Hub and the PCIe.
In order to workaround an errata of the PCIe switch we release RESET_MOCI# during the PCIe driver init unless the SW thinks PCIe is not used.
Note that USBH3 and USBH4 are not provided from the hub and thus should work.