Linux for Tegra (LT4) uses UBoot as its bootloader, replacing fastboot. In order to enable the full size USB port as 3.0, you can change the boot configuration file on the Jetson.
The boot configuration file is located here:
/boot/extlinux/extlinux.conf
There are several example configuration files in that directory which define how to boot from different devices.
The switch to change is: