I made some small changes/additions to the board.

First I had to add a USB hub. Unfortunately the Raspi could not recognize all three M5 modules at once.
Second, I made a simple HAT for the Raspi. The Raspi now has 6 GPIOs ( 2x I2C and 2xPWM) connected to the M5 modules. The Atom Hub SwitchD modules are connected to the I2C via the extra Grove port on the SwitchD. The M5StickC Plus has PWM0 and PWM1 connected to the Grove port via a low pass filter.
With this setup I am now able to simulate some sensors with the Raspi. This means I can now build a closed loop test setup where everything is controlled by the Raspi.

I also made a pull request to add the ATOM Lite to the Zephyr OS repo: https://github.com/zephyrproject-rtos/zephyr/pull/68190

And many thanks to Benjamin Cabé who prepared a large part of this board support package!