Yes at moment you can change them but for this game it was meant as bonus on certain retails like gamestop. besides bonuses this customisation of beams etc was meant toi be only available on c-store after launch so naturally they will remove it
Why sell these colors in c-store if you can cgange them for free in command line
In my opinion they should not be available anywhere but these ships that should have beams etc of that color.
Besides canon is not about simulating things. Game or not there are certain rules set by in this case CBS about what is alloved and what is not and nothing we do will not change that