Halacha is often not what we expect it to be
Our Surprise says more about us, than it says about Halacha
We begin our interaction with Gd and Life, with the premise that everything is permitted, other than that which is specifically prohibited.
Our Sages take a very dim view of those who look for unnecessary stringencies and seek to reduce the enjoyment of those things that Gd created for us to enjoy.
Why are there 2 separate and distinct decrees,
A] - Chalav Yisrael - banning unsupervised milk; and
B] - Gevinas Yisrael - banning a non-Jew's cheese?
Cheese is made from milk - if the milk is non-Kosher, surely the cheese must also be non-Kosher.
Furthermore, the decree requiring supervised milk was promulgated before the cheese decree - meaning when we were already required to monitor the milk we purchased from our non-Jewish neighbour, we were still permitted to purchase his cheese even though it was made with unsupervised non-Kosher milk!
The answer is simple enough - Our Sages' decree did not ban all milk. It was restricted exclusively to milk collected for drinking. Milk collected for making yoghurt, butter and cheese - everything that is not a liquid for drinking, was not banned.
This is not as strange as it seems. Many decrees were put on a short leash. Chazal permitted Pas Palter, bread baked by a non-Jew when it is baked for business. This does not mean breads baked by a large factory. It refers to a fellow, your non-Jewish neighbour, who has taken up the hobby of home-baking and once a week, makes a bit of money on the side by selling his breads. These are Kosher notwithstanding they've been baked in the same kitchen and oven used for his non-Kosher meals. And he need not be a vegetarian. [The Acharonim explain that the oven is Kashered each time it is heated to be used for baking]