Here's a simple counterexample, given the requirements specified. Take $N=C_3 = \langle x|x^3\rangle$, the cyclic group of order $3$, and let $H=C_5 = \langle y|y^5\rangle$, the cyclic group of order $5$. Let $\phi\in\mathrm{Aut}(H)$ be the nontrivial automorphism. You then have $G = \langle x,y\mid x^3,y^5, x^y=x^2\rangle.$
We then have $x^{y^2} = x$, so $x^{y^4}=x$, hence $x = x^1 = x^{y^5} = (x^{y^4})^y = x^y = x^2$. Thus, $x=1$ in $G$, So $\overline{N}$ is trivial.
The problem is that the assignment $\{y_1,\ldots,y_m\}\to \mathrm{Aut}(N)$ is not being asked to "reflect" the relations $\mathbf{s}$, so that forces new relation on the $x_i$. In order to get the isomorphisms, you need the assignment $y_i\mapsto \phi_i$ (which induces a group homomorphism from the free group in the $y_i$ into $\mathrm{Aut}(N)$) to factor through $H$; i.e., you really need a group homomorphism $H\to \mathrm{Aut}(N)$, not just an assignment of the generators to homomorphisms.
If you have a homomorphism $H\to\mathrm{Aut}(N)$, then the answer to both question is "yes". An "external semidirect product of $N$ by $H$" is equivalent to a homomorphism $H\to\mathrm{Aut}(N)$ (see, e.g., Exercise I.12.12 in Lang's Algebra, or the section on semidirect products (pages 167-171, especially Lemmas 7.20 and 7.21, and Theorems 7.22 and 7.23 in Rotman's Introduction to the Theory of Groups, 4th Edition), and the presentation of the semidirect product is the one you give.
If, as it happens, you have that $\overline{N}\cong N$, then the answer to your second question is "yes". Note that we certainly have $\overline{N}\triangleleft G$, there is a generating set $S$ such that $x^{-1}Nx = N$ for all $x\in S$, namely $S=\{x_1,\ldots,x_n,y_1,\ldots y_m\}$. Also, $G/\overline{N} \cong \langle y_1,\ldots,y_m,\mathbf{s}\rangle\cong H$, as that's the presentation we get if we add the conditions $x_i=1$, $i=1,\ldots,n$. So $\overline{N}\triangleleft G$, and $G/\overline{N}\cong H$ with $\langle y_1,\ldots,y_m\rangle\cong H$ in $G$, so $G\cong \overline{N}\rtimes H$. Since we are assuming that $\overline{N}\cong N$, you certainly get a semidirect product $G\cong N\rtimes H$. However, it need not be given by the action of $H$ on $N$ given by the $\phi_i$: you would need to conjugate that action with the isomorphism $\psi\colon\overline{N}\to N$.