The reflection, absorption or transmission properties of light will affect the assembly equipment. Applications can also create color demands except for green to produce the required contrast or brightness.
As FPC manufacturer knows that, alternate colors can significantly affect the identification of lead-free components, helping to avoid errors in mixed component environments.

The color of solder mask have no influence on the property of PCB itself. But, the difference among different colors is that the  resolution power of the board will be different colors such as red and blue, which phase match the resolution of the green PCB. However, the black and yellow solder masks have significantly lower resolution than the green ones, while the clear solder mask has a higher resolution.