Hatcher is unfortunately not completely clear here. The idea is to define $\tilde{H}_0(X, A)$ in such a way that you have a long exact sequence ending in $\ldots \to \tilde{H}_0(A) \to \tilde{H}_0(X) \to \tilde{H}_0(X, A) \to 0$. Given that the unreduced long exact sequence is obtain from a short exact sequence $0 \to C_*(A) \to C_*(X) \to C_*(X, A) \to 0$, it is natural to ask, seeing as $\tilde{H}_*({{-}})$ is obtained from $H_*({{-}})$ by augmenting the $C_*({{-}})$, whether one can do this by "augmenting" the whole short exact sequence, i.e. whether one can tack on a bottom level short exact sequence $0 \to C_{-1}(A) \overset{f}{\to} C_{-1}(X) \to C_{-1}(X, A) \to 0$ where $C_{-1}(A) = C_{-1}(X) = \mathbb{Z}$ from the augmentation. But $f$ must be $\mathrm{id}_{\mathbb{Z}}$ since given a 0-simplex $x \in C_0(A)$, we must have $f(1) = f(\epsilon(x)) = \epsilon(i_0(x)) = 1$ for $i_0\colon C_0(A) \to C_0(X)$ induced by the inclusion since $(\ldots, i_1, i_0, f)$ must be (the components of) a chain map, so $C_{-1}(X, A) = \operatorname{coker} f = 0$. In other words, the only way to make things work out is if the augmentation of $C_*(X, A)$ is by 0, so the homology of $C_*(X, A)$ doesn't change.
Edit: As discussed in the comments, one should explicitly note that the definition of $\tilde{H}_*(X)$ as the homology of augmentation of $C_*(X)$ does not carry over to $\tilde{H}_*(X, A)$ and $C_*(X, A)$, although it is very tempting to assume so. Instead, the only way to make "everything work out," i.e. to obtain the reduced long exact sequence, is to define $\tilde{H}_*(X, A)$ to simply be the homology of $C_*(X, A)$ as well.