Hello @mb
M5Atom Matrix has a dedicated USB-Serial chip which is not affected by the ESP32 reset and thus is keeping the serial connection alive.
In contrast the ESP32S3 inside M5AtomS3 Lite has USB built-in (and doesn't need a dedicated USB-Serial chip). The 'downside' being what you observe - resetting ESP32S3 also resets the USB connection.
Thanks
Felix