Hi,
We checked the log and the root hub got enumerated successfully:
[ 1.109380] tegra-xusb 70090000.xusb: xHCI Host Controller
[ 1.109397] tegra-xusb 70090000.xusb: new USB bus registered, assigned bus number 2
[ 1.109507] usb usb2: We don't know the algorithms for LPM for this host, disabling LPM.
[ 1.109609] usb usb2: New USB device found, idVendor=1d6b, idProduct=0003
[ 1.109616] usb usb2: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[ 1.109621] usb usb2: Product: xHCI Host Controller
[ 1.109625] usb usb2: Manufacturer: Linux 4.9.140 xhci-hcd
[ 1.109629] usb usb2: SerialNumber: 70090000.xusb
[ 1.110353] hub 2-0:1.0: USB hub found
[ 1.110390] hub 2-0:1.0: 4 ports detected
However, protocol errors found when enumerating the onboard hub. In my opinion, the issue might be related to electronic signals between the root hub port and the onboard hub.
[ 20.924584] tegra-xusb 70090000.xusb: exiting ELPG
[ 20.924954] tegra-xusb-padctl 7009f000.xusb_padctl: power on UTMI pads 1
[ 20.928374] tegra-xusb 70090000.xusb: Firmware timestamp: 2019-10-17 15:58:59 UTC, Version: 50.25 release
[ 20.928658] tegra-pmc: PMC tegra_pmc_utmi_phy_disable_sleepwalk : port 0
[ 20.928681] tegra-pmc: PMC tegra_pmc_utmi_phy_disable_sleepwalk : port 1
[ 20.928700] tegra-pmc: PMC tegra_pmc_utmi_phy_disable_sleepwalk : port 2
[ 20.929303] tegra-xusb 70090000.xusb: exiting ELPG done
[ 21.153883] usb 1-2: new high-speed USB device number 2 using tegra-xusb
[ 21.154284] usb 1-2: Device not responding to setup address.
[ 21.366225] usb 1-2: Device not responding to setup address.
[ 21.577871] usb 1-2: device not accepting address 2, error -71
[ 21.701910] usb 1-2: new high-speed USB device number 3 using tegra-xusb
[ 21.702285] usb 1-2: Device not responding to setup address.
[ 21.914257] usb 1-2: Device not responding to setup address.
[ 22.125869] usb 1-2: device not accepting address 3, error -71
[ 22.131882] usb usb1-port2: attempt power cycle
Since you have run compliance test and passed. Maybe you can check if there is hardware component(such as common choke) between roothub and onboard hub, and do hardware rework to remove them for a try?