When connected via 5VDC, that powers the board no matter what the USB is doing. FTDI is disabled unless the USB client is connected to a PC. But the FTDI is powered over the DC in that mode via the system 3.3V regulator. Powering the FTDI over USB only, requiring a 3.3V regulator to be added, might be able to be done, however, if you ever plug in the USB first, you will blow the processor on the board.
Keep in mind that the FTDI is not connected to the USB port. It is connected to the HUB that is connected to the USB port.
Now, a lot closer to this setup you describe is the BeagleBone Black. It has a connector that you can connect a USB to serial cable to. That may work better for you.
Gerald