A possible issue with custom shaders is that it would lessen the value of standard shaders. A work-around would be that certain tones/hues/effects would be only available with specific shaders. The visual FX to the Black Armoury shaders would not be obtainable, the texture from Midnight Smith, the waving smoke from Blueshfit Dreams, et cetera. On top of that, it should require obtaining a shader to unlock the colour tones tied to it.
Or it could have the opposite effect. They could break shaders down into their base sections. The color could include the textures, visual effects, metallics, fabric. So maybe instead of earning one singular shader from activities, you could earn the 4 components that would have made up the original shader!