you can add 2 daughter boards to the duet 3 main board to allow 4 PT100's to be connected.
As @deckingman said, PID tuning is currently not supported on anything but the main board but there are instructions to do it manually here https://miscsolutions.wordpress.com/2020/03/04/converting-the-e3d-tool-changer-to-duet-3-with-hemera-tools-part-2/
So in your case, its either wire back to the main board or change to PT1000's