[xerula]

The article explains X-inactivation, and it doesn't play the role you think here: both copies are broadly equally expressed among retinal cells. Also even if all cells in a retina used the same X-chromosome copy it doesn't predict color-blindness, since we would still have a trichromatic system.

The answer to the question posed by the title is simply that all mutant fourth cone types are not created equal. Most have a spectral response curve similar enough to an existing type not to make a real difference; a few have peak responses more squarely in-between those of the usual trichromat photopigments, allowing more finely graded color perception. (The article takes its time getting round to explaining this, but it's all there.)