You appear to be asking why we can't simply define $\mathbb N$ as an inductive set, i.e. a subset of $\mathbb R$ satisfying the following two axioms:
- $1\in\mathbb N$
- $(\forall x)(x\in\mathbb N\to x+1\in\mathbb N)$
The issue is that there are many sets which satisfy these two axioms. While the usual natural numbers are indeed an inductive set, so is:
- The set of positive real numbers.
- The set of positive real numbers unequal to $1/2$.
- The real numbers themselves!
Therefore, we need to add a third axiom to make our definition of $\mathbb N$ workable. One possibility, which is very similar in spirit to Munkres' definition, is the following:
- $\mathbb N$ is the "smallest" set satisfying (1) and (2), i.e. if $X\subseteq\mathbb R$ is inductive, then $\mathbb N\subseteq X$.
However, we might find it difficult to rigorously prove that there is a subset $\mathbb N$ of $\mathbb R$ which satisfies these three axioms. To get around this issue, we could instead use Munkres' definition of $\mathbb N$ as the intersection of all inductive sets, before proving that $1\in \mathbb N$ and $(\forall x)(x\in\mathbb N\to x+1\in\mathbb N)$. Then, it immediately follows from the definition of intersections that $\mathbb N$ satisfies (3).
This is in fact exercise 25 of chapter 2 of Spivak's Calculus (4th edition), page 34.