Very true, most killifish breeders I know won't even mix the same species if they are from different collection locations. On the other hand, clownfish will probably be bred to the extent guppies or bettas were because there is interest in seeing what can be made that's never been seen before. Is that wrong?
I had the neon dye injected glassfish when I was a kid too, and yes they are much different from the zebra danios that have a flourescing protein gene bred into them. Luckily they seemed to have lost favor since they are not hardy fish in standard aquaria conditions. More of a brackish fish if I remember correctly.
Unfortunately the tatooed fish are marketed to the same people that want dyed fish like Flowerhorns, people with no aquarium experience that want something brightly colored or novelty. As long as there is money to be made and people that don't know any better or care about buying them, there will be people to create the supply. Just look at all the corals that used to be dyed before the market for them disappeared because of educated hobbyists.
In the big picture it doesn't bother me too greatly, not compared to things like fish that are deep fried and still alive when served. At least the person who buys the tattooed fish may want to learn more about aquarium keeping down the road. We all started somewhere in this hobby...
