When making film transparent render layer goes gray

This is a continuation of the problem (https://blender.stackexchange.com/questions/208336/how-to-export-motioned-tracked-mesh-and-background-video-in-mp4/208356#208356) which was solved by a guy who deleted his answer thread and basically I made film transparent from the cycles render but while in cycles render the render layer goes gray and when I go back to blender render the background goes back to gray. Hopefully that’s helpful if not comment what info you need! How do I get both in the final export and properly tracked on?