Poppa, DY, & Ubiquitin
We need to separate out the stomach piercing issue (which is not a problem for CY because those cows are not used) and Rav Shachter’s problem (which applies to all milk).
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.
I personally asked Rav Shachter about his problem. He told me that treifos are a miyut hamatzui in cows (which is why we check the lungs) which is well over 1/60 (he did not say that treifos are a rov). He said in Europe and the early days of America where milk came cow by cow you could say kol d’porush m’ruba porush and drink milk. Nowadays that it is all mixed together and we know a miyut hamatzui of that milk is treif, he doesn’t know how we can drink the milk. Rav Schachter said that he has been searching for years for a satisfactory answer to this problem.
Poppa, your question about R’Meir is a very good one. I will try and investigate to see if there some discussion as to how R’Meir ever drank milk.
R’Yehuda could drink milk as long as it wasn’t mixed together with that of many other cows, because of kol d’porush. Meat isn’t a problem because when the cows are shechted we check the only treifa that is a miyut hamatzui.