You are mixing up "waste material" with "material waste". The parent was making a point about cost. It's cheaper not to feed male baby chicks. It's cheaper to raze the forest. It's cheaper to let cows fart.
There are externalized costs to these things, but they don't really affect the prices that people are going to pay for the produce, at least not directly. I guess you can charge a small markup for being "green" (or pretending to be).
Now maybe a cow is only "3% efficient" in terms of calories, but the calories it takes in are really cheap and the calories it puts out are prized. It's a profit deal! In engineering, higher efficiency generally is more expensive and the economic optimum is never the efficiency optimum.
Except for the poop lagoon crisis https://newrepublic.com/article/151242/behind-hurricane-flor...
the dangers of cow farts https://www.businessinsider.com/bill-gates-warns-cow-farts-c...
Or the "waste" baby male chicks who are ground alive when they are a day old (graphic) https://www.youtube.com/watch?v=BQ5qAfyUuWE
Or the rain forests wasted to make room for more cows https://www.onegreenplanet.org/animalsandnature/beef-product...
Or that it takes 100 calories inputs to beef production to get 3 calories out. (Beef is 3% efficient). https://iopscience.iop.org/article/10.1088/1748-9326/11/10/1...