This is an embarrassingly simple question, but I realized that I haven't formalized the following idea in my mind.
Suppose we have a function $f: \Bbb{R} \to \Bbb{R}; x \mapsto x$. What am I to make of the notation $f(x-1)$? Is it "the same function" applied to a different argument? Is it a "different function?"
Is it a function at all? If $f(x-1)$ is the name of a function (in particular, a name for $x \mapsto f(x-1)$, where the latter $f(x-1)$ should not be confused with the former), then it ought to take an argument: $f(x-1)(y) = y-1$. It is not the same kind of creature as $f(x)$ (which is a function application), but is comparable to just $f$.
And yet I sometimes read things like "suppose we transform the function $f(x)$ into $f(x-1)$" in physics. It's not hard to understand what's being said, but the lack of formality in my thought is troubling me for some reason.

I think the most straightforward way to regard it is just as a function composition, which is formally defined as $(f \circ g)(x) = f(g(x))$ (taking note of well-definedness in the respective domains). So in your specific example, let $g : \mathbb{R} \to \mathbb{R} : x \mapsto x - 1$, then $f(x - 1) = (f \circ g)(x)$.
And yes, to add to your additional questions, the composition of two functions is again a function, assuming the composition is well-defined. If you had a function from apples to oranges, and a function from oranges to pears, then you could have a composition from apples to pears which is well-defined, but not a function from oranges to oranges.