The link above is has the only information I have about the bootloader. Referring to the schematic for the Due, it looks like USB port AB (native port), D+ and D- are connected to the Sam, while USB B (programming port) connects to the 16U2 processor on the Due board. The 16U2 is connected to TX0 and RX0.
Since the Arduino IDE can program the DUE through either USB port, it would be worth trying to connect directly, but I have no knowledge as to whether it would work. Note that the DUE schematic includes resistors and over voltage protection in its connection between the USB plug and the SAM.