The role of capillary pores percolation and gel pores are investigated to explain the underlying differences between relative diffusivity obtained from different experimental techniques using microstructures generated from two different types of hydration model viz., CEMHYD3D (a voxel based approach) and HYMOSTRUC (a vector based approach). These models provide microstructures with different capillary pore connectivity for the same degree of hydration and the same porosity due to the underlying assumptions. In order to account for a C-S-H diffusivity at the micro-scale, a continuum micro-mechanics based model has been proposed. These simulations show that deperolation of capillary pores at around 20% of capillary porosity is essential in order to correctly predict diffusivity of cement paste with water-cement ratio by mass (w/c) in between 0.4 and 0.5. Furthermore from our analysis we present a viable postulate that the higher diffusivity measured by electric resistivity compared to other methods is due to differences in contribution from gel pores. For electrical resistivity measurement it is proposed that all gel pores are diffusive whereas for ion and tracer transport it is proposed that only nitrogen accessible gel pores are diffusive.