The recipe you are referencing implies the adding of the milk in 2 different stages. This is because that is the way we do it in the mountains. The fresh morning milk is added directly into the vat, the culture added and cream from the evening milk melted and blended into it. The rest of the evening milk is then added. Since the evening milk is cool, it will lower the temperature quite a bit. We always tried to warm the first round in such a way that when we added the second round of milk, it would be just at the right temperature for adding the Rennet. But the milk is only chilled to maybe 45 to 50 degrees, not cold.
I imitate this practice in the more in depth recipes, because I think it has an affect on the quality of the cheese. I would feel safe to say this overheating, cooling, then reheating has a definite effect on the bacteria cultures within the cheese, and I would also guess that it would have an effect on the enzymes and protein structures in the raw milk.
But if you are doing a hobby cheese make, and aren't so in depth to care about these minute details then its fine if you skip this double initial heating, and just heat up once, and let incubate about 20 minutes. As far as bacteria count goes, this will be about the same. And if you are using pasteurized milk then this technique won't matter anyway. There are no wild bacteriae contend with, and the enzymes and proteins are already thoroughly screwed up.