When X is a concept in widespread mathematical use, the answer to the question "What do model theorists mean when they talk about X?" is always going to be "Exactly what all other mathematicians mean when they talk about X." Model theorists do mathematics in exactly the same way (with the same foundations) that number theorists and topologists do.
So: to a model theorist, "$A$ is countable" means "$A$ can be put in bijection with $\mathbb{N}$".
The root of your question is an unfortunate ambiguity in the quoted claim. (Where did you find it, by the way? You should always cite your sources.)
The correct interpretation of "The Peano axioms don't imply a countable set of natural numbers" is "There exists a model of $\mathsf{PA}$ (the first-order theory Peano Arithmetic) which is not countable". That is, there exists $N\models \mathsf{PA}$ such that there is no bijection between $N$ and $\mathbb{N}$. This is a precise mathmematical statement - there's no circularity here. Maybe it seems circular to you because you think that the point of the theory $\mathsf{PA}$ is to define $\mathbb{N}$? This is a misconception. Theories don't define structures, they only describe their properties. At most, they can characterize them uniquely up to isomorphism, but first-order logic can only do that when the structure is finite. Model theorists have access to $\mathbb{N}$ (e.g. defined in set theory as the least inductive set) just like all other mathematicians.
You are correct, by the way, that there is a second-order theory $\mathsf{PA}_2$ such that (when we use the standard semantics for second-order logic) $\mathbb{N}$ is the unique model of $\mathsf{PA}_2$ up to isomorphism. In this case, instead of "The second-order Peano axioms imply a countable set of natural numbers", it would be more precise to say "Every model of the second-order Peano axioms is countably infinite".