Cross-breeding allows nature to combine things that fit together in all of the right places. And we just don't know how that even happens, or why. We don't understand nature's algorithm for DNA. No even the tip of the iceberg.
Sure, nature isn't always correct, but does thing properly 99.999% of the time. And that's good enough.
It is utterly incomparable to GM done by humans ~ genes are inserted, but the results are not equivalent to what is done by nature, because we don't understand DNA enough to know where we should be placing the inserted DNA, so that things don't massively fuck up inexplicably somewhere down the line.