As to why, it's essentially what's explained here in Lesson 1's ellipses section. The further away from the viewer the circle in 3D space is, the greater the angle at which we see it is (meaning, it opens up more, allowing us to see a wider ellipse).

That said, while it's understandable that students will want to understand the logic that drives these relationships and truths, it's not actually something that helps very much - it may provide some comfort, but still tends to distract the student by shifting their energy and attention to understanding what's going on on a conscious level, rather than focusing on consciously applying the rules as they're provided. In other words, just like the complex concepts explained in Lesson 1's boxes section relating to how the vanishing points slide along the horizon, a student consciously understanding that is not what's important. What's important is that the students consciously and mindfully work to apply the rules - for example, ensuring that their sets of parallel edges in 3D space are drawn such that they converge towards a shared vanishing point.

I completely understand that this seems backwards - we're used to learning academic topics, where understanding is everything, but learning to draw is much more like a sport. Understanding the logic that underpins it all doesn't actually get you closer to being apply it, but focusing on that conscious understanding will delay you getting to the exercises. And it's in the exercises that we rewire the instincts embedded into our subconscious.

It's that subconscious that we rely upon when drawing our own stuff, outside of the structure of a course or exercise. We don't want to use our conscious cognitive resources towards that (trying to think through how every individual edge should be plotted, the specific degree of each ellipse, etc) because that will leave very little for the creative decisions of design, composition, and narrative. Instead, we rely on our subconscious auto-pilot to handle all of that, and the subconscious is not trained through understanding - it's trained through highly intentional repetition. That is, going through the exercises repeatedly over a long stretch of time, while being deeply intentional in terms of how that exercise is to be approached.

What you're describing above, that your instincts tell you something that contradict what the instructions of the exercises does, is entirely normal. After all, the purpose of what we're doing here is retraining and rewiring your instincts to make them more reliable - but that's not going to come from understanding the theory. It's going to come from investing the time to ensure that whenever you draw a cylinder, and specifically when you draw the farther end of that cylinder, that you are consciously and intentionally telling yourself, "this ellipse needs to be wider than the one I drew for the closer end".

And over time, that will sink into your instincts so that outside of this course, without thinking, that is what you will do naturally.

Of course, while one could certainly still dive into the theory behind it all, in this course we don't - it'd demand way more resources than we're able to bring to bear (given our focus on making our instruction as affordable as we can) for something that we've found does not allow students to learn better or more efficiently. And so instead, we focus on shifting the attention to the exercises, to applying their instructions as intentionally, consciously, and thoroughly as possible.

While I don't expect that's a satisfying answer, it is what will produce results. Complete the revisions, and focus on applying those instructions as intentionally as you can. Don't rely on your instincts here.