Our FAE provided a solution for this problem. To start the USB 2.0 test pattern generation on the LS1046A via u-boot, you have to enter these commands:
usb start
mw.l 3100420 0
mw.l 3100430 0
mw.l 3100020 0
mw.l 3100424 50000000
mw.l 3100020 1
These are the commands for USB 3.0 controller 3. Change the offset to the following for accessing the other USB ports
USB3.0 controller 1 --> 2F0_0000 - 2FF_FFFF
USB3.0 controller 2 --> 300_0000 - 30F_FFFF
USB3.0 controller 3 --> 310_0000-31F_FFFF
The state of the USB_ID Pin seem to have no effect on the test pattern output