Very cool effect! Work pretty well.
Unfortunately, as every shader in C2, the rendering pass is made before the upscale. So if you use Low quality fullscreen scaling, the visual result will be affected.
(Why using the low quality? Because when you do a retro game in low res, the fullscreen high quality upscale is very very very greedy. Using the low quality is visually very close, and sooo much faster, as long as you don't play too much with shaders. )
Of course it's not your fault. It's related to the C2 rendering process. And it won't change.