does this work with modded planets or does it only affect vanilla planets

Ok I made a quick edit to show the difference between Shadowed Atmospheres and this.

https://imgur.com/gallery/difference-between-two-starbound-mods-oVopMDL

i with the light on the planet would change depending on were the sun is

Неплохо задумано, но очень темно)

Both mods replace the same files, as the shadows are simple textures with transparency.

So does it work together with Shadowed Atmospheres or how?

Now this is based

This is basically the Shadowed Atmospheres mod but better

Yes, this mod is different from that one:
Shadowed Atmospheres
Because that one just darkens the atmospheric halo, while this mod darkens the shadows themselves and removes the halo in the shadows.