I have endorsed all puppies in every litter I have bred (since 1995), and removed them when appropriate. that is when all health testing has been carried out, and the owners aware of their ongoing responsibilities if they breed.
I believe that all puppies should automatically be endorsed and it be an opt out Rather than opt in when registering puppies.
Also with breeds which have DNA tests there may need to be a method of lifting an endorsement on a per litter basis, if the animal is a carrier, to ensure if bred from it is used suitably.
Maybe the KC should endorse all pups from untested parents 'progency not elgibile for registration' automatically. I am not a breeder as I only keep dogs but I have family who do breed every 3-4 years. All pups are endorsed with progency not elgibile for registration and the not for export. The new owner has to sign to say that they understand the written explanation as to why these are placed on the pup. The breeding one is to prevent the people using the animal as a breeding machine or being sold on as one, although it will not stop the litters they can't be registered. The export one is to stop them acting as a third party for someone abroad, although again it wont stop them if they really wanted do. Both of these can be lifted after 2-3 years by mutual agreement of the owner and breeder.