"Take factory farmed chickens for example. I do know that output in a factory farm is higher compared to that of a traditional farm, 6 weeks of maturity compared to ~ 3 months. Yet, it's hard to deny the quality of taste of a well farmed bird. And in being the most obese country in the world, should high output be our end game?"Good question. But I think it hinges on a couple of assumptions that aren't necessarily taken into account. Firstly, the decision of what is food, and what is to be produced isn't really entirely decided on a country government basis, at least here in the US, although it is dramatically affected by such things as the Farm Bill and other regulations. But I'd like to point out that the nature of "quality of taste" is one of perspective and preparation, and not an absolute.
Take, for example, my recent visit to esteemed old/new Vietnamese restaurant, Cafe TH. Pictured above, I had ordered the bo kho, which is the Vietnamese style beef stew praised by the Houston Press article. Compared to other, perhaps more traditional preparations, this broth was more delicately flavored, but by no means a wimp. But a few things struck me as odd. First, carrots are part and parcel of this dish, and here, Cafe TH opted to use baby carrot sticks instead of the traditional hunks of older, cheaper carrots. Secondly, that the meat used was indeed, "good meat" - mostly muscle, and trimmed of fat. These are not elements that fit well in a preparation that will be stewed for extended periods of time. The carrots were mush. The meat came across as being dry, and I was missing the unctuousness evident from gelatin extracted from bone and gristle. I wanted to praise the balanced spicing of the dish, but, in retrospect, it was a disaster in terms of texture.
(One tangent - the chef opted not to serve the traditional selection of Vietnamese herbs and mints with soup. I was uncertain if this was an attempt at non traditional service, but I know the soup could have used the herbal zing.)
Which returns me to the point about the chicken. We can't evaluate the quality of an ingredient independent of the targeted preparation. There are preparations where a factory farmed bird is more appropriate than free range bird. And vice versa. And perhaps the real skill of a cook is no better demonstrated than a less than optimal ingredient is converted into a delectable dish.