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: usb_port_owner_info=2 #USB 3.0
There are two usb_port_owner_info=0 specifications in extlinux.conf, one is extra. Only the last assignment will be used. You may delete one of the specifications, as I've shown in the following example.
A new example config file with USB 3.0 enabled:
TIMEOUT 30
DEFAULT primary
MENU TITLE Jetson-TK1 eMMC boot options
LABEL primary
MENU LABEL primary kernel
LINUX /boot/zImage
FDT /boot/tegra124-jetson_tk1-pm375-000-c00-00.dtb
APPEND console=ttyS0,115200n8 console=tty1 no_console_suspend=1 lp0_vec=2064@0xf46ff000 video=tegrafb mem=1862M@2048M memtype=255 ddr_die=2048M@2048M section=256M pmuboard=0x0177:0x0000:0x02:0x43:0x00 vpr=151M@3945M tsec=32M@3913M otf_key=c75e5bb91eb3bd947560357b64422f85 usbcore.old_scheme_first=1 core_edp_mv=1150 core_edp_ma=4000 tegraid=40.1.1.0.0 debug_uartport=lsport,3 power_supply=Adapter audio_codec=rt5640 modem_id=0 android.kerneltype=normal fbcon=map:1 commchip_id=0 usb_port_owner_info=2 lane_owner_info=6 emc_max_dvfs=0 touch_id=0@0 tegra_fbmem=32899072@0xad012000 board_info=0x0177:0x0000:0x02:0x43:0x00 root=/dev/mmcblk0p1 rw rootwait tegraboot=sdmmc gpt