For a pseudo-Anosov flow
$\varphi $
without perfect fits on a closed
$3$
-manifold, Agol–Guéritaud produce a veering triangulation
$\tau $
on the manifold M obtained by deleting the singular orbits of
$\varphi $
. We show that
$\tau $
can be realized in M so that its 2-skeleton is positively transverse to
$\varphi $
, and that the combinatorially defined flow graph
$\Phi $
embedded in M uniformly codes the orbits of
$\varphi $
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 the closed orbits of
$\varphi $
after cutting M along certain transverse surfaces, thereby generalizing the 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
$\varphi $
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.