Lattice Boltzmann method (LBM) is an efficient tool to perform direct numerical simulation of gas flow in micro-size pores. Despite great advances in LBM and its use in describing gas flow in micro-size channels in slip and transitional flow regimes, exploring formulations that are able to capture flow behavior in domains with complex boundary geometries remains a challenging task. As a result, the impact of complexities in pore structures on gas flow may not be fully explored using LBM. In this study, we propose to use the combined bounce-back and Maxwellian diffusive reflection scheme to capture the slip velocity with a new set of slip coefficients. Optimal values of slip coefficients are determined using a gradient based method, where the results from the linearized Boltzmann equation is used as the reference solution. The proposed formulation is further validated against predictions from molecular dynamics simulation in the presence of complex geometries by introducing obstacles of different shapes in straight channels. LBM with the proposed boundary treatment is then used to investigate gas flow in a synthetic microscopic permeable medium. Results indicate that gas exhibits different flow configurations as Knudsen number varies, and apparent gas permeability appears to have up to a second-order dependency on the reciprocal mean pressure in slip and transitional flow regimes.