The uncalibrated microcontroller temperature on the Duet 2 (WiFi and Ethernet) should be within 13C of the true temperature. For the Duet 3 MB6HC is could be up to 39C out, and for Duet 06 and 085, it could be up to 45C out. The microcontroller used in Duet 3 Mini does not have a working MCU temperature sensor.

To calibrate the temperature sensor:

1. The whole of your printer must be at room temperature. So do this after leaving the printer turned off for a long time, e.g. overnight.
2. Turn your printer on
3. As quickly as possible (before the Duet has time to heat up), connect to it using Duet Web Control and read the temperature from the CPU Temp. box on the Machine Control page. Call this Tc.
4. To determine the current room temperature, read off the extruder heater and bed temperatures and take an average. If you have a PT100 sensor on the extruder, use just the extruder temperature because it is likely to be more accurate. Alternatively, use a thermometer to measure room temperature. Call this Tr.
5. Send command M912 P0 S# where # is (Tr - Tc). It may be negative. Assuming you did not already have a M912 command in config.g, after a few seconds the CPU temperature should then read about the same as room temperature.
6. Add that M912 command to your config.g file. It doesn't matter where, but I put it near the end, before the M501 command and the T0 command.

mcu-temp in Duet3 Mini5+

Unfortunately the SAME54P20A chip used in the Duet 3 Mini does not have a functioning temperature sensor. In theory it does have an on-chip temperature sensor, but the errata document for the chip says it doesn't work.

Due to this you would be unable to monitor the MCU temp in order to control fans. The driver sensors do work for fan control, but only return flags of warning and overtemp, so fine grained control of fan speed would not be possible with a separate thermistor.