Provocative article and thanks for posting.....
I cull pups, humanely (vet puts them to sleep), and always have, even back when I was raising Catahoulas (mostly white headed pups were usually deaf so were put down). I have culled recently for a bad bite and a little female puppy that had a hip damaged in the womb and never outgrew it, and by six weeks it was obvious, she'd be lame. The rest of the pups in the litter made the cut. One had borderline overshot bite but vet said he was confident his adult teeth would come in better so he went to a wonderful home up in Oregon.
I have a female Spanish Mastiff with bad tibias (note: out of HD rated A parents too, so much for saying A hips = no problems, not hardly)...that developed when she was around 4-5 mos old. I won't breed her in spite of the fact that she's a massive, beautiful girl - I would not dare chance that she'd throw even one pup with bad rear knees or legs. Her hips were good (we x rayed), it's down lower in her left rear leg. Anyway, she can get around well, is an excellent guard and goat guardian, and is my 'house potato' who gets to sleep in the house when she wishes. Breeding inferior dogs together will only produce inferior specimens. Soundness is so important.
But so is type. Breeding say, a Spanish Mastiff of very little type, skin and wrinkle to another like dog, will only serve to take away some of the breed's most cherished characteristics. If in turn pups from that cross are bred to likewise less typey dogs, soon, you are breeding oversized Labs....or a facsimile of one! And losing cherished points of a true mastine.
There has to be a balance. I had another SM female I opted not to breed, due to lack of type, size, and an unpredictable and somewhat sullen temperament. Plus, she chased and mauled goats. Was out of working dam too. I gave her to another rancher who has her more for a pet and house guard not livestock guardian. And, three of the best guards I have here in SM's are out of show ring stock, that don't work. But their pups are fabulous top notch livestock guards. Go figure.
I think outcrossing is key now and then to any successful breeding program and hybrid vigor cannot be denied when you cross breeds together for F1 crosses.