[guided]The assignment is complex-linear because for all $\alpha,\beta\in\mathbb{C}$ and all $f,g\in S_2(\Gamma_0(N))$,
\begin{align*}
\omega_{\alpha f+\beta g}
&=2\pi i\,(\alpha f+\beta g)(z)\,dz \\
&=\alpha\,2\pi i\,f(z)\,dz+\beta\,2\pi i\,g(z)\,dz \\
&=\alpha\,\omega_f+\beta\,\omega_g.
\end{align*}
Now check that the two constructions undo each other. If we start with a cusp form $f$, construct $2\pi i f(z)\,dz$ on $\mathcal{H}$, descend it to $X_0(N)$, and pull it back again along $\pi$, the pullback is the original invariant differential $2\pi i f(z)\,dz$. Since $dz$ is nowhere-vanishing on $\mathcal{H}$, this recovers the original function $f$.
Conversely, if we start with a holomorphic differential $\omega$ on $X_0(N)$, pull it back to $\widetilde{\omega}=2\pi i f(z)\,dz$, and then descend that invariant differential, the descended differential has pullback $\pi^*\omega$. The quotient construction gives uniqueness of the descended differential with this pullback, so the result is exactly $\omega$. Hence the map
\begin{align*}
S_2(\Gamma_0(N)) \longrightarrow H^0(X_0(N), \Omega^1_{X_0(N)}), \qquad f \longmapsto \omega_f,
\end{align*}
is a complex-linear bijection, and this is the claimed natural complex-linear isomorphism.[/guided]