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Abstract Detectable electromagnetic counterparts to gravitational waves from compact binary mergers can be produced by outflows from the black hole-accretion disk remnant during the first 10 s after the merger. Two-dimensional axisymmetric simulations with effective viscosity remain an efficient and informative way to model this late-time post-merger evolution. In addition to the inherent approximations of axisymmetry and modeling turbulent angular momentum transport by a viscosity, previous simulations often make other simplifications related to the treatment of the equation of state and turbulent transport effects. In this paper, we test the effect of these modeling choices. By evolving with the same viscosity the exact post-merger initial configuration previously evolved in Newtonian viscous hydrodynamics, we find that the Newtonian treatment provides a good estimate of the disk ejecta mass but underestimates the outflow velocity. We find that the inclusion of heavy nuclei causes a notable increase in ejecta mass. An approximate inclusion of r-process effects has a comparatively smaller effect, except for its designed effect on the composition. Diffusion of composition and entropy, modeling turbulent transport effects, has the overall effect of reducing ejecta mass and giving it a speed with lower average and more tightly-peaked distribution. Also, we find significant acceleration of outflow even at distances beyond 10 000 km, so that thermal wind velocities only asymptote beyond this radius and at higher values than often reported.