It is ironic that the fluorescent color is the most ethical part of this fish's breeding. The process of inserting GFP or one of its variants is practically harmless and done routinely on zebrafish, with e.g. lox/cre back in the day and CRISPR in modern times. The gene itself has no real long-lasting effects.
But when all is said and done, you end up with one batch of fluorescent fish. How do you get to the point where you can sell them? Well, you inbreed them. And inbreed them. And inbreed them. You may have heard about e.g. neon tetras being fragile because most of the captive population descends from a small number of animals collected from the wild decades ago, with no fresh blood in all that time. GloFish are the same, except even more extreme. It is hardly surprising that shortbody forms and other mutations emerge when their genetic pool is a puddle.