We re-evaluate the extragalactic gamma-ray flux prediction from dark matter annihilation in the approach of integrating over the nonlinear matter power spectrum, extrapolated to the free-streaming scale. We provide an estimate of the uncertainty based entirely on available N-body simulation results and minimal theoretical assumptions. We illustrate how an improvement in the simulation resolution, exemplified by the comparison between the Millennium and Millennium II simulations, affects our estimate of the flux uncertainty and we provide a best guess value for the flux multiplier, based on the assumption of stable clustering for the dark matter perturbations described as a collision-less fluid. We achieve results comparable to traditional Halo Model calculations, but with a much simpler procedure and a more general approach, as it relies only on one, directly measurable quantity. In addition we discuss the extension of our calculation to include baryonic effects as modeled in hydrodynamical cosmological simulations and other possible sources of uncertainty that would in turn affect indirect dark matter signals. Upper limit on the integrated power spectrum from supernovae lensing magnification are also derived and compared with theoretical expectations.