Have you tried upgrading to Qubes 4.2 yet? Your descriptions above sound just like my experience with the D16. However, since installing 4.2 my onboard USB never works for my mouse (I have to boot with it in the onboard USB and switch to a PCI USB card after boot to use my mouse). And any USB connections for powered devices cannot be shared outside of sys-usb.
I have more details here: USB device and PCI Sound card issues persistent with 4.2-rc4