My colleague Mai Gehrke found a positive answer to my question: if $f : X \to Y$ is an initial morphism of Top over Prost, then $X$ is equipped with the initial topology defined by $f$.
Proof. Let $f: X \to Y$ be an initial map.
Step 1. Let $x,y \in X$. If $f(x) \leqslant f(y)$, then $x \leqslant y$.
Consider the cofinite topology on $\mathbb{N}$ and let $g: \mathbb{N} \to X$ be the map defined by $g(0) = x$ and
$g(n) = y$ if $n > 0$. Since the specialization order defined by the cofinite topology is the equality relation, $g$ is a monotone map. Let $h = f \circ g$. Then $h(0) = f(x)$ and $h(n) = f(y)$ if $n > 0$. I claim that $h$ is continuous. Indeed, let $U$ be an open subset of $Y$. Since $f(x) \leqslant f(y)$, the condition $f(x) \in U$ implies $f(y) \in U$. It follows that $h^{-1}(U)$ is either equal to $\emptyset$, $\mathbb{N}$ or $\mathbb{N} - \{0\}$ and hence is open in all cases, which proves the claim. Since $f$ is an initial map and $g$ is monotone, $g$ is continuous. Thus if $V$ is an open subset of $X$ containing $x$, $g^{-1}(V)$ is an open subset of $\mathbb{N}$ containing $0$. Therefore $g^{-1}(V)$ is cofinite and contains some $n > 0$. It follows that $y = g(n)$ belongs to $V$. Thus any open subset containing $x$ also contains $y$, that is, $x \leqslant y$.
Step 2. Let $\mathcal{T}$ be the topology on $X$ and let $\mathcal{I}$ be the initial topology on $X$ defined by $f$. Since $f$ is continuous, $\mathcal{I} \subseteq \mathcal{S}$. Let $i: (X, \mathcal{I}) \to (X, \mathcal{S})$ be the identity map. Then $f \circ i:(X, \mathcal{I}) \to Y$ is continuous by definition of the initial topology. Moreover, suppose that $x \leqslant_\mathcal{I} y$. Since $f \circ i$ is continuous, it is monotone with respect to the specialization orders and hence $f(x) \leqslant f(y)$. It follows by Step 1 that $x \leqslant_\mathcal{T} y$. Thus $i: (X, \mathcal{I}) \to (X, \mathcal{S})$ is monotone and since $f$ is initial and $f \circ i$ is continuous, $i$ is a continuous map from $(X, \mathcal{I})$ to $(X, \mathcal{S})$. It follows that $\mathcal{S} \subset \mathcal{I}$ and finally
$\mathcal{S} = \mathcal{I}$. Thus the topology on $X$ is the initial topology defined by $f$.