For certain pseudo-Anosov flows ϕ on closed 3-manifolds, unpublished work of Agol-Guéritaud produces a veering triangulation τ on the manifold M obtained by deleting ϕ's singular orbits. We show that τ can be realized in M so that its 2-skeleton is positively transverse to ϕ, and that the combinatorially defined flow graph Φ embedded in M uniformly codes ϕ'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 ϕ'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 ϕ 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 cutopen 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.