RepRapFirmware (as at version 3.3.1) for Duet 3 currently has the following limitations when tool boards or expansion boards are used.

We do not intend to remove these in future firmware versions.

• After upgrading firmware on an expansion or tool board, its configuration settings are lost. You must restart the main board, or at least re-run config.g. Duet Web Control usually restarts the main board automatically after auto-installing firmware on an expansion or tool board..
• A heater on an expansion or tool board can only be controlled by a temperature sensor on the same expansion board. This is a safety precaution.
• Filament monitors must be connected to the same board as the corresponding extruder motor.

We have no plans to remove the following limitations, although removing them would be technically possible.

• A thermostatically-controlled fan on an expansion board can only be controlled by a temperature sensor on the same expansion board.
• Z probes connected to expansion or tool boards are limited to types 8 and 9.
• DHT temperature/humidity sensors connected to expansion boards are not supported

We plan to remove these in future firmware releases.

• Filament monitors for extruders driven by expansion boards and tool boards are not yet supported. Support is planned in release 3.2.0. [Implemented in 3.2beta3]
• Software reset data is not available for expansion boards. This is planned for release 3.2.0. [Implemented in release 3.2beta1]
• Heater tuning is not yet supported on expansion or tool boards (M303). Support is planned in release 3.3. For now, use the manual turning procedure instead.
• The main board does not react to heater faults on expansion boards by pausing the print.
• Endstop switches and Z probes connected to the main board cannot control motors on an expansion board. This is planned to be fixed in release 3.4.
• If you use a Z probe then the Z motors must be connected to the main board. This is planned to be fixed in release 3.4.
• Stalls of expansion board motors are not yet reported and cannot be used for homing.
• Change of stepper driver status on expansion boards are not proactively reported (but can be queried using M122). e.g. Overheat warnings, short to ground etc.
• MCU temperatures and monitored voltages on expansion boards are not yet reported in the object model (but can be queried using M122).