There are several problems that can occur when cross breeding, or breeding. The harlequin great danes may be born deaf, just like many white cats can...
Also the are several characteristics that animals have in terms of shape size etc... For example trying to use sperm from a charolais bull (which is developed for meat) to a holstein cow (which is developed for milk) may cause injuries to the cow, simply because the size of the head of the unborn veal is larger than the one from the holstein baby.
When I mentioned why we keep cats, dogs birds etc... I simply meant that these animals did not naturally develop to kept indoors. We did it for our needs (be it security, pleasure, whatever).
So in the same way that we cross breed dogs, cattle, cats to get specific body structures, colours, etc.. in the same way these scientists cross breed fish and use science to get a specific outcome.
Is it ok to do it in order to get leaner, better looking, faster growing veals and fish?
Is it ok to do it in order to get faster growing , more yielding crops?
Is it ok to do it in order to get stronger, taller, better looking dogs?
Is it ok to do it in order to get better looking flowers?
Then why it is not ok to do it in order to get glowing fish?
IMO, ethical dilemas are answered by a yes or a no. There are no yes but.... If you use bioenginnering for one cause, then you may use it for everything. Because then the problem that arises is who decides for what we can use it?