Breeding for a flaw?

I had a chance to read a little bit on here today and see all the discussions about where all our dogs come from and about folks breeding for different uses and characteristics.
I've thought about and discussed it quiet a bit about what exactly makes a catchdog or baydog or any other working dog do what he does? With catchdogs, What makes a dog do something that everything in his genetics and instincts and mother nature is telling him NOT to do.. In nature, an animals instincts tell him to survive so if that means to flee or run that's what they do.. The wolf that our dogs are said to all come from will in the wild always choose survival over death. So how is it that we have bred a dog that will go against everything that his instincts should be telling him to do the opposite of ?
I think that all bulldogs and any dog that will die on a hog or doing any other work is genetically flawed. The APBT is the result of hundreds of years of breeding on a genetic flaw..
I'm all for crossing dogs and trying to breed the exact type of dog you want and can use.. And I believe there is always room for improvement. But I also think that if you take some dogs that go against their natural instincts and will catch and hold something no matter what even if it means death and you breed those dogs long enough to get that consistently. Then in about 100 years you will have an APBT...