First off, I should say I disagree with the premise of the question. Nonhuman entities don’t breed plants and animals for agricultural production. Humans do―plant breeders, scientists, farmers...and the list goes on. Does anyone really think if they walk into an agricultural facility that the only things to be found inside will be dollar bills and lawyers? GMO, conventional or organic plant breeding and research have decades of research and trials behind a product that growers can readily purchase.
To the point of whether we can do better than nature, which has spent eons and not mere decades perfecting crops and animals, I would have to say, for the intended purposes, yes, we sometimes can. Without regard to production method, humans have been tailoring crops and animals to their liking for thousands, if not millions, of years. Not every variety or every breed is suited to every situation. I’m pretty sure there aren’t wild herds of Jersey cows running across the fruited plains.
Corn is another example. Corn as we know it does not really exist in nature, yet it is a staple grain across the globe. What everyone recognizes as corn today is the result of thousands of years of selective breeding going back to a plant called teosinte, which barely looks like corn. In more recent history, most corn hybrids have been bred to have upright leaves versus droopy leaves, because upright leaves intercept sunlight better.
Norman Borlaug is credited with saving a billion lives or more because of his research with wheat resulting in crosses with high yields and disease resistance.
As for the idea that humans aren’t part of nature, at least not in the way a redwood tree would be viewed as part of nature, I would argue that agriculture itself is not natural. Once you start lining up plants in rows and assisting them in their fight against weeds, pests, bugs and even precipitation, or fence in livestock to shelter them from predators, I don’t think that’s quite the same as hunting and foraging while living in a cave.
With GMOs, we aren’t doing things nature doesn’t do already. Herbicide resistance exists in nature. The most obvious example is spraying a lawn with 2,4-D to kill dandelions. The grass doesn’t die. Cereal rye kills weeds with an herbicide of its own creation. Are biotech crops made to express traits they don’t normally have? Yes. Breeders also employ mutagenesis techniques, even in organic crops. The genetic manipulation of the things we grow isn’t limited to biotechnology.
I’m inclined to believe it is human nature that keeps driving innovation forward.