When it comes to rendering, a connection is opened between Harmony and the rendering engine - in this case Maya Softrender.
Maya Batch is opened in the background, and the information from the Harmony scene file is sent to Maya. All the information needed, including the animation on the model and the position of the camera, is sent to Maya. Maya Batch then opens in the background and the original .mb file is opened. This file should match the FBX model in size, but may have a higher polygon count, a more advanced texturing setup, or even a more advanced set of shaders. Since the full Maya scene is loaded, you can use any shader, lighting setup, and texture that Maya Softrender supports.
The opened scene file repositions the model inside based on the information provided from the Harmony scene file. For consistent lighting effects, you may want to parent the lighting rig to the model so it is also repositioned along with the model.
The frame is then rendered and sent back to Harmony to be composited there. The data comes back into Harmony as a series of Maya .iff images. These images contain not just image data, but also depth information, and Harmony will use this depth information to properly clip any 2D layers that are interacting with the 3D model in the Harmony scene, resulting in a perfect composite without the need to track any masks.
You can also apply any effects that are supported on bitmaps to the rendered sequence, such as blurs and blending modes.