RepRapFirmware doesn't currently provide a standby mode. You can turn off the motors, heaters and fans to mimise the direct load from the VIN supply, but there isn't yet the facility to put the microcontroller itself into a low-power state. However, your RPi may draw more power than the Duet's processor, unless you can put it into a low power standby mode.
You could switch the power to the Duet, either using a SSR to switch the VIN input (if you still want to supply power to your 5V converter), or by switching the AC input to the PSU.
Another way would be to control the enable pin to the 5v regulator on the Duet. You can get at this pin via the 5V_EN jumper block. But you would need to take steps to put the TMC2660 drivers into standby first because the are powered from VIN.
