I use the graduated nd filter in the Color Efex pro 4.0 plugin. It is easy to adjust. When you save the image, the setting will be retained in lightroom or PS's filter memory until you change it again. So, just apply it to every frame.
Lightroom is a tool for graphical interaction with images rather than batch processing. For your use case Imagemagick looks better suited. There is also a tutorial for this: http://www.imagemagick.org/Usage/compose/#divide