That command affects the dwc_otg controller, not the xhci controller. You should be able to use "uhubctl" to power off the ports.
The Ethernet port on Pi4 is independent of anything to do with USB.
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sudo apt-get install pciutils sudo setpci -s 01:00.0 0xD4.B=0x41
Does the Pi reboot successfully if you unplug everything except ethernet and power? (i.e. unplug all other peripherals during the shutdown phase)