The fact that the atlas using $x \mapsto x^{1/3}$ on $\mathbb{R}$ is diffeomorphic to the trivial atlas using $x \mapsto x$ on $\mathbb{R}$ highlights my ignorance of diffeomorphisms and atlases.

Other differential topologists should weigh in on this to confirm or deny, but as a differential topologist I have never come across the notion of a diffeomorphism between two **atlases**, or even two smooth structures. Moreover, what you have here is not two atlases but two charts. These may seem like picky points, but if you find yourself getting confused then one good technique to learn is to sharpen your definitions. By that, I mean be a bit more careful about distinguishing between things that although often used synonymously are actually distinct.

So you have two charts, $x \mapsto x^{1/3}$ and $x \mapsto x$. As both of these have image $\mathbb{R}$, they each define an atlas: $\{x \mapsto x^{1/3}\}$ and $\{x \mapsto x\}$. Each of these atlases then defines a smooth structure on $\mathbb{R}$. Each of these smooth structures defines a smooth manifold with underlying topological space $\mathbb{R}$. Although each of these constructions follows in a unique way from the previous step, technically each is a different thing.

Back to the confusion about diffeomorphisms. We talk of two atlases being **equivalent** if they generate the same smooth structure, or if they define the same smooth manifold. In concrete terms, we can test this by looking to see if the **identity** map is smooth in both directions (using the atlases to test smoothness).

But I can have inequivalent atlases that nonetheless define diffeomorphic manifolds. This is because the condition of being *equivalent* is stronger than that of defining diffeomorphic manifolds. Equivalence rests on the smoothness of the identity map (in both directions), the manifolds being diffeomorphic rests on the smoothness of *some* map (and its inverse). So although the two atlases given are inequivalent, they define diffeomorphic manifolds because I'm free to take the map $x \mapsto x^{1/3}$ and its inverse to define the diffeomorphism.

It's a good exercise to help with sorting out the definitions to check that you really understand why these two manifold structures on $\mathbb{R}$ are diffeomorphic. That is, write down the map and write out its compositions with the transition maps and **see** that it works.