"Naturally homogenised" milk is a bad description. Milk fat floats around in milk in something called "globules" (yes, it's a technical term :-) ). There is a membrane that acts kind of like a bag that holds the fat. In cow's milk from modern, milking cows the globules are big. Because fat is lower density than water, it naturally floats to the surface over time.
You may wonder why it doesn't just rocket up to the surface in a few seconds. The reason for this is "brownian motion" (also a technical term :-) ). In things like liquids and gas, small particles are kind of floating around everywhere. Small particles bump into each other causing mostly random motion. Imagine that you are headed for the toilets at a crowded bar. You make a bee-line to the door, but every time you try to make a step, somebody bumps into you. You end up wandering all over the room. If there are enough people wandering around energetically enough, you may never make it to the toilet. In fact, if someone were to take a video of you, they might not even be able to tell that you were trying to get there since you keep bouncing off of random people.
That's kind of what's happening in the milk. You have these fat globules and they are floating to the surface of the milk, but they keep getting bumped by other particles. The bigger the fat globules, the more energy they have to make it to the surface. Also, the bigger they are, the less influence each of those bumps have. Milk with very large globules will have the cream rise to the top very quickly. For milk with very small globules, the cream will never rise.
Homogenised milk is made with the same goal: to have a milk where the cream does not rise. However it is accomplished in a very different way. In homogenisation, the membranes in the globules are broken. The causes the fat to leak out. Because the fat is sticky, it coats the milk protein bundles and never rises to the top. In reality, there *is no cream* in homogenised milk. The fat is just coating the protein bundles.
Homogenisation causes a lot of problems in cheese making. Because the fat coats the protein bundles, it makes it very difficult for the rennet to react with those protein bundles. This makes a *very* weak curd set in rennet formed curds. You basically have lots and lots of protein bundles that will not set and so the curds do not form a good, strong bond with each other. There is nothing you can do to fix this problem. Additionally, because the fat is more accessible in the final cheese, it is more susceptible to being broken down by lipolysis processes. This causes potential funky flavours and aromas as the cheese ages. On the plus side because the fat is all stuck to the protein, virtually all of it ends up in the cheese, which gives you more yield.
TL;DR: No. It's not naturally homogenised. It just has much smaller fat globules that don't rise to the top of the milk. This gives you a milk where the cream doesn't separate, but which is great for cheese making (as opposed to homogenised milk). The reason we don't use this wonderful milk commercially is because of economics (much lower milk yield by these breeds even though the milk quality is dramatically higher in many cases).
