Because the CH340 drives RX to ~4.5v it doesn't communicate with the Duet 3. To remedy this you need to either cut the trace or de-solder the pad on the CH340(green) or on the ATMega(red). I would suggest de-soldering the pad on the CH340 because it's easier.

In addition to the current wiring schematic you'll also need to to connect the TX from the Arduino to RX on the duet

Arduino RX > Duet 3 io1.out

Arduino TX > Duet 3 io1.in

Arduino GND > Duet 3 io1.GND

After the modifications you will no longer be able to upload a sketch using the USB port. You have to use a FTDI serial adapter and connect it to the 6 header pins next to the USB port.