The Galactic Center Excess (GCE) of GeV gamma rays can be explained as a signal of annihilating dark matter or of emission from unresolved astrophysical sources, such as millisecond pulsars. Evidence for the latter is provided by a statistical procedure---referred to as Non-Poissonian Template Fitting (NPTF)---that distinguishes the smooth distribution of photons expected for dark matter annihilation from a clumpy photon distribution expected for point sources. In this paper, we perform an extensive study of the NPTF on simulated data, exploring its ability to recover the flux and luminosity function of unresolved sources at the Galactic Center. When astrophysical background emission is perfectly modeled, we find that the NPTF successfully distinguishes between the dark matter and point source hypotheses when either component makes up the entirety of the GCE. When the GCE is a mixture of dark matter and point sources, the NPTF may fail to reconstruct the correct contribution of each component. We further study the impact of mismodeling the Galactic diffuse backgrounds, finding that while a dark matter signal could be attributed to point sources in some outlying cases for the scenarios we consider, the significance of a true point source signal remains robust. Our work enables us to comment on a recent study by Leane and Slatyer (2019) that questions prior NPTF conclusions because the method does not recover an artificial dark matter signal injected on actual Fermi data. We demonstrate that the failure of the NPTF to extract an artificial dark matter signal can be natural when point sources are present in the data---with the effect further exacerbated by the presence of diffuse mismodeling---and does not on its own invalidate the conclusions of the NPTF analysis in the Inner Galaxy.
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