The only difference?
Creating GM organisms is a completely different order of biological tinkering than the selective breeding and cross-breeding methods it seeks to supplant. Breeding is merely a way to sort out desired characteristics from the existing gene pool of related organisms - GM methods often combine genes from organisms which aren't even remotely related.
Our knowledge of genetics is much too incomplete at this point to make the claim that we have a "far better understanding of the outcomes" of GM realistic; there may be unintended consequences we won't learn of for many years. Turning the products of this infant technology loose upon the world is incredibly reckless.
