I've completely rewritten this question, in accordance with this advice.
As a motivating example, suppose we're working in ETCS. Let $\bar{1}$ denote the canonical singleton set, and assert that by $x \in X$ what we really mean is that $x : \bar{1} \rightarrow X$ is a function.
Now let $f : X \rightarrow Y$ denote a function and suppose $x \in X$. Then $f \circ x \in Y$.
That's all well and good, but there's - not a problem, exactly, but more like an inconvenience.
Suppose the symbols $0,1,2,...$ are defined to be elements of the set $\mathbb{N}$. So for example, we have that $2 \in \mathbb{N}.$ In other words, we have that $2 : \bar{1} \rightarrow \mathbb{N}$. Suppose also that we define $f : \mathbb{R} \rightarrow \mathbb{R}$ by asserting that $f \circ x = x^2$. The inconvenience is that $f \circ 2$ is ill-defined, because $2$ has codomain $\mathbb{N}$, while $f$ has domain $\mathbb{R}$.
The solution, of course, is to view $2$ as an element of $\mathbb{R}$, rather than $\mathbb{N}$. Technically what we've done is chosen a "canonical" injection $\chi : \mathbb{N} \rightarrow \mathbb{R}$. Thus $2$ can be used as an abuse of notation for $\chi \circ 2$, and therefore $f \circ 2$ can be viewed as an abuse of notation for $f \circ \chi \circ 2$.
That was a motivating example, but the inconvenience is more general.
For instance, a metric space does not have open sets. However, a topological space has open sets, and thankfully there is a canonical way of obtaining a topological space from any metric space. Thus we may speak of "the open sets of $(X,d)$" rather than "the open sets of $f(X,d)$," where $f$ is a functor $\mathsf{Met} \rightarrow \mathsf{Top}$.
So what I'm looking for is a systematic way of being rigorous about these kinds of abuses of notation. A reference would be nice.
