For certain pseudo-Anosov flows $phi$ on closed $3$-manifolds, unpublished work of Agol--Gueritaud produces a veering triangulation $tau$ on the manifold $M$ obtained by deleting $phi$s singular orbits. We show that $tau$ can be realized in $M$ so that its 2-skeleton is positively transverse to $phi$, and that the combinatorially defined flow graph $Phi$ embedded in $M$ uniformly codes $phi$s orbits in a precise sense. Together with these facts we use a modified version of the veering polynomial, previously introduced by the authors, to compute the growth rates of $phi$s closed orbits after cutting $M$ along certain transverse surfaces, thereby generalizing work of McMullen in the fibered setting. These results are new even in the case where the transverse surface represents a class in the boundary of a fibered cone of $M$. Our work can be used to study the flow $phi$ on the original closed manifold. Applications include counting growth rates of closed orbits after cutting along closed transverse surfaces, defining a continuous, convex entropy function on the `positive cone in $H^1$ of the cut-open manifold, and answering a question of Leininger about the closure of the set of all stretch factors arising as monodromies within a single fibered cone of a $3$-manifold. This last application connects to the study of endperiodic automorphisms of infinite-type surfaces and the growth rates of their periodic points.
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