I may not know what I'm talking about (always a bad thing to do) but this is something carried out on adults and on differentiated cells, yes? Therefore, there is no likelihood of "He grew gills or his hair changed colour as we watched" is there? The hair colour change would only grow in. The sinister government super soldiers can't grow an extra arm or an eye in the back of their heads, but would merely have bulked up muscles and greater stamina? There is no suggestion of germ cells being modified, so no passing changes on to the next generation? No modification of embryos, or any modification of the many adult stem cells adults still have?
In which case, I have less of a problem, I think. Is there a difference between permanent genetic hair colour change and dyeing hair, except that dyeing hair uses toxic and dangerous chemicals? Same argument for prolonging the onset of baldness or grey hair. There will be a great demand for that because there is already one with all kinds of weird procedures that are not medically tested. If these procedures are licensed and medically supervised, then from a public health viewpoint it has to be better, right? Tattooing and body modification is now socially acceptable.
I'd even go so far as to say that skin-lightening and skin-darkening in this way is safer than applying chemicals like Mercury and should probably be allowed. The problem, as you have identified already, is unlicensed procedures, without medical supervision. However, this is already a problem even without gene therapy being available. The Body Builders who take steroids and human enzymes to stimulate muscle growth, and the Transhumans who split their tongues down the centre to become lizard-like are going to use these techniques to modify their bodies even further. There is little that can be done to stop them if that is what they wish to do. There will always be an illegal supplier where there is a demand. The public health crisis that will be created in the future is going to be expensive to deal with.
However, there is no suggestion that we are permanently altering the gene pool - no selective breeding of humans in the way that domestic cats and dogs are now bred? Or am I wrong?