When it comes to rendering, what happens at that stage is that a pipe is opened up 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 all sent to Maya. Maya Batch then opens up 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 Harmonyas a series of Maya .iff images. These images contain not just image data, but also depth information, and Harmonywill use this depth information to properly clip any 2D layers that are interacting with the 3D model in the Harmonyscene, 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, blending modes.