The apple genome has 50,000 genes. (The human genome has only 30,000). Crossing any two parents, these genes will assort differently each and every time. And, yes, that is exactly what breeders do: make thousands of crosses, (I have seen figures as high as 10,000 needed to select a desirable cross), and then grow them out and find new desirable fruit. (Takes many years!) There is a scientist in our local research station who is attempting to identify the genes in parents responsible for specific characteristics, then screen the progeny of crosses to make sure these particular genes are present in the offspring, hopefully avoiding having to wait until the trees have grown to pick out likely good ones. (And, no, I am not a fan of his work, particularly since he has recently swerved into active genetic manipulation.)
The alternative is to let nature make the thousands of crosses needed, and just pick out the ones which are desirable to humans. (Any apple with "Pippin" (eg. Cox's Orange Pippin) or "Seedling", (Bramley's Seedling), were just such random crosses. So was the venerable McIntosh, which arose on the farm of Alexander McIntosh in Duneddin, Ontario back in the 1800's. He mowed it down 4 times, sprouting anew each time, at which point he is purported to have said, "Well if thee will live, let thee live".
Broomholm OrchardZone 5b in Nova Scotia