A signed tree model of a graph $G$ is a compact binary structure consisting of a rooted binary tree whose leaves are bijectively mapped to the vertices of $G$, together with 2-colored edges $xy$, called transversal pairs, interpreted as bicliques or anti-bicliques whose sides are the leaves of the subtrees rooted at $x$ and at $y$. We design an algorithm that, given such a representation of an $n$-vertex graph $G$ with $p$ transversal pairs and a source $v \in V(G)$, computes a shortest-path tree rooted at $v$ in $G$ in time $O(p \log n)$. A wide variety of graph classes are such that for all $n$, their $n$-vertex graphs admit signed tree models with $O(n)$ transversal pairs: for instance, those of bounded symmetric difference, more generally of bounded sd-degeneracy, as well as interval graphs. As applications of our Single-Source Shortest Path algorithm and new techniques, we - improve the runtime of the fixed-parameter algorithm for first-order model checking on graphs given with a witness of low merge-width from cubic [Dreier and Toruńczyk, STOC '25] to quadratic; - give an $O(n^2 \log n)$-time algorithm for All-Pairs Shortest Path (APSP) on graphs given with a witness of low merge-width, generalizing a result known on twin-width [Twin-Width III, SICOMP '24]; - extend and simplify an $O(n^2 \log n)$-time algorithm for multiplying two $n \times n$ matrices $A, B$ of bounded twin-width in [Twin-Width V, STACS '23]: now $A$ solely has to be an adjacency matrix of a graph of bounded twin-width and $B$ can be arbitrary; - give an $O(n^2 \log^2 n)$-time algorithm for APSP on graphs of bounded twin-width, bypassing the need for contraction sequences in [Twin-Width III, SICOMP '24; Bannach et al. STACS '24]; - give an $O(n^{7/3} \log^2 n)$-time algorithm for APSP on graphs of symmetric difference $O(n^{1/3})$.