@jersmi actually the fill is behind in both combine 3D layers if I'm right, but it seems it's the ovals & lines that are stacked differently (even if for example the points are on top of the lines in both Combine 3D Objects" nodes).
If you want to get rid of the Z position for 3D objects, you can use Karl Henkel's Parabox Convert 3D Object to Layer nodes !
@jersmi don't know if you mean you wanted to fill the composition you shared, but using Smokris reinterpret you can fill it, but straight edges, without the round point edges (except for the 2 points on start).
For the oval shaded points size, I don't know ! But what I don't understand is that using the same color, the lines and ovals don't have the same color (you'll see it better in this modified composition toggling between 2 and 30 points, on 2 points, the left oval point clearly has not the same color, although the line is unlit shaded and the oval shader ignores lightning).