The key difference between the M and MLX is that the MLX comes with a top board with the programmable LED array and integrated motion sensor (6 Degrees of Freedom). Both the M or MLX have the same footprint of 52x24mm with the MLX having a slighting taller profile of 13mm.
The DUO M is the core camera board with both image sensors and the USB controller while the MLX has the M base board as well as an additional top board to extend functionality. Beyond the top board the MLX also ships with IR bandpass filters that match the 850nm LEDs to assure only IR light is allowed into the sensors.
The M is best if you need to be able to experiment with different lens types or will only be using the sensor in a passive mode (no illumination).
The MLX is best in scenarios where you must control and limit the lighting conditions. This is common in most computer vision algorithms as it provides a simple way to guarantee consistent aspects of a scene.
To learn more about the differences make sure to check out the DUO Comparison page.