I have a loose understanding of what coordinates are, but not something rigorous or concrete. For example take the statement of this result below 
When the author says let $x = (x^1, \dots x^n)$ denote the "standard coordinates" on $U$ and $y = (y^1, \dots, y^m)$ those on $\widetilde{U}$ what precisely does the author mean?
For example there is a very clear and rigorous definition of what a basis for a vector space is, but I can't seem to find that for coordinates. The closest thing I know to a definition for coordinates is the following:
If I have a smooth manifold say $M$ of dimension $n$ and a smooth chart $(U, \phi)$, then for any $p \in U$ we have $\phi(p) = (x^1(p), \dots, x^n(p))$ where the $x^i : U \to \mathbb{R}$ are the component functions of the homeomorphism $\phi$ and the collection of component functions $(x^1, \dots, x^n)$ are called local coordinates on $M$.
However this notion doesn't seem to apply to the corollary above, because it seems "coordinates" take on a different meaning above, because for example $$\frac{\partial G^i}{\partial y^k}$$ (in the statement of the result above) doesn't make sense since $y^k$ interpreted this way would actually be a function and it's meaningless to take the partial derivative of a function with respect to another function.
Furthermore the only definition of the partial derivative of a function that I'm familiar with is the following
Definition: Let $U \subseteq \mathbb{R}^m$ be an open set and let $f : U \to \mathbb{R}$. The $j$-th partial derivative of $f$ at $a$ is defined to be the directional derivative of $f$ at $a$ with respect to the basis vector $e_j = (0, \dots, 1, \dots, 0)$ (where $1$ is in the $j$-th position) provided the derivative exists $$\frac{\partial f}{\partial x^j} = \lim_{t \to 0} \frac{f(a +te_j) - f(a)}{t}$$
and in this definition above I just think of $x^j$ as a reminder that I'm taking the directional derivative with respect to the $e_j$ basis vector on $\mathbb{R}^m$.
How do I reconcile the definition above with what the authors mean by standard coordinates?
Basically the question I'm asking is, what does
"let $x = (x^1, \dots, x^n)$ denote the standard coordinates on $U$"
mean? Or more generally if $V$ is an open subset of $\mathbb{R}^k$ what would
"let $z = (z^1, \dots, z^k)$ denote the coordinates on $V$"
mean?
About convention/notation:
The formalized version of this expression is
Note that the expression references, tacitly, some ambient manifold and a chart (which is usually clear from context).
Of course, an equivalent version of this is defined in your post, but I'm stating it here in order to fully address your concern about the Corollary. Also, the above expression is often used where the manifold is smooth (and so is the chart).
About Partial Derivatives:
Firstly,
Here is how it is defined:
I left out a lot of details, as well as the path toward motivation for its definition, for brevity (and focus) of this post. To see these details and why the above is well-defined, see Chapter 3, "Tangent Vectors", of the text (see the section "Computations in Coordinates" in particular).
Note that in the above, you're not "differentiating with respect to" $z^i$ (which is senseless in this context as you've mentioned), you're just using $z^i$ in the notation to reference the chart you're defining the operator with.
This is helpful for your question because in the case of the Corollary, the expression
means
so that if $f \in C^\infty(U)$ then using the above definition of partial derivatives we have that for $x \in U$,
That is, in the case where $U$ is given standard coordinates, the operation is the same as the regular partial derivative operator. The $x^i$ on the left corresponds to coordinates on $U$, and the $x^i$ on the right corresponds to the notation used for the definition of the regular partial derivative operator in $\mathbb{R}^n$. For further clarity,
Thus, for the case of the notation within the Corollary,
where the $x^k$ on the right corresponds to the notation used for the regular $k^{th}$ partial derivative in $\mathbb{R}^m$.
Caveat: