Yep. Basically, I stay away from processed foods designed to make foods shelf stable. They all have issues. Hydrogenated fats are not truly digestible because our enzymes do not fit the created molecule of fat. Our bacteria also lack the enzymes to digest these fats. Obviously, there is a logic to pasteurization. There is a danger in storing and drinking raw milk, but we know much more about how to prevent these problems these days than pre-WWII for example. Refrigeration is much more prevalent. Our ability to keep dairy equipment clean and sterile is much better. And like other means of creating stable shelf life, there are health costs to pasteurization. I now live in a state where it is legal to sell raw dairy in your own store. In other words the dairy has to own the store. Fortunately, there are some local sources for me to obtain raw dairy, and I can get raw goat milk and raw A2 cow milk.
You already seem to know a lot of this. The pasteurization process destroys the natural enzymes such as lactase. For this reason I stopped drinking “milk” years ago as I became lactose intolerant. But, it also destroys the natural bacteria present in order to destroy the harmful ones. It also seems to affect certain vitamins, and then defatting the milk removes the fat soluble vitamins, which is why they “fortify” milk. The truth is except for the danger of harmful bacteria, natural milk is simply healthier, and is in the form nature designed for use.
In terms of mineral content, they are largely the same. I don’t know of any data showing the protein is different. However, for the above reasons, and some new ones I have come to believe, I simply have stopped almost all “American” dairy. The A1 casein is a real problem for me, and seems to inflame my prostate. So, not only do I not drink A1 milk, but I’ve had to stop eating cottage cheese, etc. I also now believe, although cannot prove, that it is a primary cause of T1 diabetes here in the U.S. Lastly, pasteurized dairy is a major source of oxidized dietary cholesterol, which I now believe is a contributing factor in heart disease. For these reasons I just have eliminated pasteurized dairy mostly from my diet. I now have the occasional ice cream, and still have hard cheeses. For me it has little to do with micro or macronutrients.