The advantage is, it works and it's cheap.
If you are using a coldlight, although it is diffuse, there needs to be a more full diffusion or you will see the grid in your image. If the diffusor is in contact with the negative's top surface, newton rings cannot form because of the location of the diffusor and how newton rings form. So it's not that the top material is plexi and the bottom material is glass, it's that its a diffuse source in contact with your neg and coherent reflections cannot form. Newton rings don't form on the bottom, because the negative on the bottom is not smooth enough to allow the surfaces to get close enough together to get coherent reflections. It also reduces dust problems above the negative.