Transport characteristics of the stochastic magnetic boundary of the Large Helical Device (LHD) are investigated, based on three-dimensional Monte-Carlo Braginskii-type fluid model code, EMC3, coupled with the kinetic neutral transport code EIRENE, in direct comparison with experimental observations for aspects of the relation between the magnetic topology and the resulting transport in terms of counter acting flux tube flows and impurity screening/transport. Divertor probe measurements show a rather weak divertor parameter dependence on upstream density in contrast to those of tokamaks at high-recycling regime. This is found to be due to the loss of parallel momentum via cross-field interaction between the stochastic flux tubes, where strong flow shear exists. The three-dimensional modeling predicts an impurity screening potential of the stochastic scrape-off layer (SOL) at high densities. The remnant island geometry affects the energy transport, which leads to suppression of the thermal forces by increasing cross-field energy flux across islands at high collisionality. The screening effect is most pronounced at the edge surface layers with a strong friction force exerted by the background plasma flow, where the flow toward divertor is enhanced due to the rich ionization source. Modeling results are compared to the edge carbon emission obtained in experiments, where a reasonable agreement on the density dependence is found, indicating the existence of the impurity screening mechanism in the stochastic SOL of LHD.