I think making it 3d already means that there will be more than 2 colors/shades of a color. Because of the shadows and stuff. And i dont think unity skyboxes are allowed if they arent a solid color and you are counting it as one of two colors that you have
Nah you can do 3d and keep it in in 2 colors, I know because I debated on it but I work in Unreal and there's no easy browser export. I don't use Unity but I imagine you'd have to modify the skybox or modify the camera post processing to posterize down to 2 colors.
So long as there are only two colors on screen, you can do whatever you want