With regard to the stomach piercing problem, where records are kept and the company KNOWS which cows are treifos, I don’t see how we could deliberately turn a blind eye. A Rav at that point in the process could not pasken on that cow that it is mutar when he knows that the company has records of it being a treifa.
He’s not there when it’s milked, so he’s not “turning a blind eye”. I don’t know that the company’s “yediyah” is halachically significant.
This is why the problem might be worse, potentially, for CY milk (except that AFAIK they remove those cows for CY milk).