Your dog is genetically engineered. Your tomato. Your children. And I don't mean in the lab, but the usual way, by using your intelligence to choose suitable stock and then breeding until you get what you want. The shortcut in the lab is just faster and cheaper, not different in any basic or ethical way.
But that old-time genetic engineering still plays by the rules of nature, so to speak. Grafting branches between trees is pushing it a little. Splicing genes, not to mention synthesizing them from scratch, I think is pretty clearly of a different nature.
Golden delicious apples were a sport. Any really new feature in evolution is. The advantage of doing it in the lab is, its lots safer. You know what you're getting - just what you wanted. Not all the other random accidental changes you couldn't measure. Grandma's better tomato could actually make you sick - she had no idea what she was doing and no control over the process.
It has the potential to be different in the way that building a 747 is different than breeding a bird to be able to carry people across the Pacific Ocean. Either may be possible, but it's different.
I don't understand, you will never create a 747 with bird genes. In fact, they can do nothing with this technology that could not have been done by infinite monkeys with gene-splicing equipment. The only difference I see is the speed.