Your understanding is correct in this regard. The recommendation is to use the external power jack (J8) to avoid the short circuit. Unfortunately, this is a shortcoming in this kit design and I have passed it along. But if you use the external JTAG debugger like J-Link, Olimex connector, would recommend you to switch to the power jack for providing supply to the kit.
Looking at the schematics, I don't see how using the external power jack (J8) would avoid the short circuit in any way?
FT2232HQ seems to be active and initialized regardless of how the board is powered.
The only reasonable possibility I can see is to solder a wire from the RESET# input of FT2232HQ to GND.
My bad. They are directly tied to 3.3V Connecting the RESET# (14) to GND seems like the only option left.