Thanks for the tip @flypeek
I checked with my Hello World code and this worked.
I did not expect the AtomS3 to be that different to the original AtomMatrix. However I just confirmed if I change the "board" to just
M5Stack-Atom all the original code compiles.
I would have expected big changes if we referred to the ESP32-C3 with the new RISC architecture, but the S3 was fairly similar I thought.
I presume it has a new board definition due to the LCD screen on the AtomS3. If I can get the Zigbee unit working nicely, I might port the example over and post up a PR in the AtomS3 library.
Many thanks again @flypeek you have unblocked me and I can keep moving forward (I hope).