Numerical modeling of gas flows in rarefied regimes is crucial in understanding fluid behavior in microscale applications. Rarefied regimes are characterized by a decrease in molecular collisions, and they lead to unusual phenomena such as gas phase separation, which is not acknowledged in hydrodynamic equations. In this work, numerical investigation of miscible gaseous mixtures in the rarefied regime is performed using a modified lattice Boltzmann model. Slip boundary conditions are adapted to arbitrary geometries. A ray-tracing algorithm-based wall function is implemented to model the non-equilibrium effects in the transition flow regime. The molecular free flow defined by the Knudsen diffusion coefficient is integrated through an effective and asymmetrical binary diffusion coefficient. The numerical model is validated with mass flow measurements through microchannels of different cross-section shapes from the near-continuum to the transition regimes, and gas phase separation is studied within a staggered arrangement of spheres. The influence of porosity and mixture composition on the gas separation effect are analyzed. Numerical results highlight the increase in the degree of gas phase separation with the rarefaction rate and the molecular mass ratio. The various simulations also indicate that geometrical features in porous media have a greater impact on gaseous mixtures’ effective permeability at highly rarefied regimes. Finally, a permeability enhancement factor based on the lightest species of the gaseous mixture is derived.