Nonlinear 3D MHD simulations and validations reveal that the hybrid particle-MHD transport is a key process for driving the pump-out in the presence of Resonant Magnetic Perturbations (RMPs) in the KSTAR tokamak. Particle transport and the resulting density pump-out by RMPs are shown to be composed of not only the classical flow convection near magnetic islands due to polarization but also the neoclassical ion diffusion across perturbed magnetic surfaces. The latter is known as the Neoclassical Toroidal Viscosity (NTV) and is integrated into nonlinear MHD simulations here for the first time, revealing that the two-stage pump-outs observed in KSTAR experiments are reproduced only with such integrated nonlinear MHD and transport evolution. Near-resonant responses, which have received less attention than the resonant response, play distinct roles in the pump-out along with the island formation. In addition, this modeling is used to investigate the pump-outs in double-null-like plasmas and numerically capture the effect of the double-null shape on the pump-outs, which may explain the difficulty of Edge Localized Mode (ELM) suppression access in double-like plasmas. This reveals new aspects of the impact toroidal geometry and mode coupling have on 3D physics and reveals the importance of near-resonant components in suppressing ELMs.