I have something of a conundrum with the Pi 3 Model B. A late requirement in my project needs me to disable power on the USB ports, and enable power later at a particular point with a script.
I have a separate system connected via a USB cable which powers the system. When the raspberry begins to boot up, it takes about 3 seconds from when the boot up begins until the other system sees power form the USB. Further, when I reboot the raspberry with sudo reboot, power from the other system is cut off for a few seconds, then switches back on during the boot (at about the same time). This heavily implies that there should be some software/firmware level control for power on the USB-ports, but for the life of me I can't find it.
I have tried sudo sh -c 'echo 0x0 > /sys/devices/platform/soc/3f980000.usb/buspower, but all that seems to do is completely disable communication on the ports. Power is still being applied afterwards.