Disclaimer: I am not an algebraist so I do not have a "professional" perspective on this.
Suppose (1) you are only concerned with polynomials as functions, and (2) you are only concerned with situations where the correspondence between lists of coefficients and functions is one-to-one. For specificity, let's say you only care about polynomials with real coefficients, as functions on $\mathbb{R}$.
[This is a huge restriction, as algebraists are not only concerned with polynomials as functions, and as your example shows, there are situations where the correspondence is not one-to-one. And for better or worse, definitions of algebraic objects as given at the university level tend to reflect the needs of future algebraists, not the general mathematical public. But let's ignore this.]
Given your perspective (1) and (2), in defining a polynomial, you have at least two choices:
One, to define a polynomial as a certain kind of function. In short, "A polynomial is a function from $\mathbb{R} \to \mathbb{R}$ whose rule can be expressed in a certain form." In more detail, you might say "a polynomial is a function $f: \mathbb{R} \to \mathbb{R}$ with the property that there is a nonnegative integer $n$ and a list of real numbers $c_0, \dots, c_n$ with the property that $f(x) = \sum_{j=0}^n c_j x^j$ holds for all real $x$."
Two, to specialize the algebraist's definition to the case of $\mathbb{R}$. (Define a polynomial "formally", point out how a formal polynomial induces a function, and then define "polynomial function" from that.)
Granting (1) and (2) above, these are both perfectly fine definitions. The first, in particular, is given in every high school level book, and every university level calculus book, that I have ever seen.
The second has obvious drawbacks--- if you only care about polynomials as functions--- because what a polynomial "is" has been divorced from its corresponding function. One must prove, for example, that if two polynomials induce the same function, they are the same polynomial. Why be bothered?
Given (1) and (2), this is a valid point and I cannot really argue against it. But I can argue that the first definition also has drawbacks. To the extent that it seems easier or more "natural", I'd argue it is because we generally meet it first, and therefore have a much longer time to get used to it. (If you ever teach beginning algebra, you will be cured of the idea that any definition of polynomial is "natural" to most people.)
Consider the notion of the degree of a polynomial, which hopefully you agree is a useful notion. How to define the degree? Well, if $f$ is given by a formula $f(x) = \sum_{j=0}^n c_j x^j$, and $c_n$ is nonzero, then it's this number $n$ appearing in the formula.
... but is why is this well defined? How do we know that $f(x)$ can't be given by two different expressions, $\sum_{j=0}^n c_j x^j$, and $\sum_{k=0}^m d_k x^k$, with $c_n \neq 0$ and $d_m \neq 0$ and $n \neq m$? We can get around this in at least two ways:
We can say that the degree of $f$ is the minimal possible value of $n$, over all conceivable formulas $x \mapsto \sum_{j=0}^n c_j x^j$ that could represent the rule of the function $f$. This makes the definition of the degree very easy, but does not make degrees easy to compute. (By this definition, we know that $x^5 + 3x + 1$ certainly has a well defined degree, and that it is at most $5$. But to know that it is equal to $5$ we need to know that no expression $\sum_{j=0}^4 c_j x^j$ can give rise to the same function. How do we know that?) This feeds into the second way of defining the degree:
We can prove that if the rule of $f$ can be given by a formula $\sum_{j=0}^n c_j x^j$, with $c_n$ nonzero, then $n$ is uniquely determined, so it makes sense to say the degree of $f$ is that value of $n$.
Even if you don't care about the degree, you will run into this issue. Roughly speaking, whenever you want to conclude that two polynomials aren't the same because they don't have the same list of coefficients--- and not by explicitly exhibiting a value of $x$ for which they don't evaluate the same--- you run into this technicality.
I don't mean to imply that it's a particularly arduous issue to deal with. It's possible to give short proofs that the degree is well-defined. My point is only that it requires proof. High school textbooks (and university-level calculus books) generally circumvent this issue by ignoring the fact that it requires proof. Lots of things become more "natural" if you treat them this way.
I'm not saying we should all be "for" the second definition or "against" the first. But I'd argue that however you deal with the actual issues involved in defining polynomials, even for polynomial functions $\mathbb{R} \to \mathbb{R}$, you are dealing with the "list of coefficients" vs "function" distinction whether you want to or not. It is not something you avoid with the first definition of "polynomial", and introduce arbitrarily with the second. It is always there. So it's no mystery that some people prefer to build it into the definition. That is how I think about it anyway.