I've been self-teaching myself differential geometry and still somewhat new. As I understand it, a local coordinate chart on an $n$-dimensional, real, smooth manifold, $M$, is a pair $(M_{(q)},q)$ where $M_{(q)}\subset M$ is some region (the coordinate domain) and
$$ q=(q^1,\dots,q^n):(M_{(q)}\subset M)\to (\mathbb{R}^{n}_{(q)} \subset \mathbb{R}^n) $$
is a local diffeomorphism from the coordinate domain to its image $\mathbb{R}^{n}_{(q)}:=q(M_{(q)})\subset \mathbb{R}^n$.
When trying to conceptualize various things about manifolds and geometry, I often use the 2-sphere $S^2$ as my go-to playground for working through ideas and, when using coordinates, I always use the "usual" coordinates $q=(\theta,\phi)$. However, the 2-sphere is usually also one of the first examples given in any introductory source on manifolds and they always provide the stereographic projection coordinates as an example of a local coordinate chart (that's fine, I'm not confused about that). But I don't think I've ever seen the usual $(\theta,\phi)$ given as an example of local coordinates and it seems like that would be the obvious first example. Is this just because authors assume it's already familiar to everyone and not worth mentioning?
Perhaps I have not been exposed to sources that do give $(\theta,\phi)$ as local coordinates on $S^2$, but then there was this shocker: I saw in Abraham and Marsden's "Foundations of Mechanics'' when they use $(\theta,\phi)$ in the usual way but briefly mention that they are "not true coordinate functions" (I don't remember the exact quote). If that is the case, then I have misunderstood the hell out of everything from the beginning and need to backtrack a lot.
So, what's the deal? Are $(\theta,\phi)$ just too-obvious-to-mention local coordinates on $S^2$ or have I misunderstood everything?