Dear FDEV, I have a suggestion for implementing this and potentially many other features further down the road: introduce submodule slots for all modules, then change the weapon colour modifier from a "global" option to a submodule that you can install in the colour slot of each individual weapon. I suggest this because having that support in the game would potentially enable so much more customization using the same mechamism, e.g., there could be purchasable weapon modifiers (like RNGineer effects but with known attributes instead of random), DSS could become an addition to the discovery scanner instead of its own module, or perhaps all scanners could be submodules of the sensors package, there could be a universal limpet controller with varying number of "program slots" for controlling different types of limpets, etc.
(Edit: Note that I'm not saying all of the above would need to be done, just that a "modifier slot" system would technically open up lots of possibilities for future features using a familiar interface.)