In this work a non-conservative balance law formulation is considered that encompasses the rotating, compressible Euler equations for dry atmospheric flows. We develop a semi-discretely entropy stable discontinuous Galerkin method on curvilinear meshes using a generalization of flux differencing for numerical fluxes in fluctuation form. The method uses the skew-hybridized formulation of the element operators to ensure that, even in the presence of under-integration on curvilinear meshes, the resulting discretization is entropy stable. Several atmospheric flow test cases in one, two, and three dimensions confirm the theoretical entropy stability results as well as show the high-order accuracy and robustness of the method.