We report the results of modelling the transport of n-octane and n-hexadecane and their mixtures through carbonaceous nanopores at high-pressure conditions. Pores are modelled as smooth slit sheets with perturbations added as ridges and steps and a version of the Statistical Associating Fluid Theory (SAFT-γ Mie) is used both as equation of state and as a coarse-grained force field to account for fluid-fluid and fluid-solid molecular interactions. Molecular simulation allowed the description of transport diffusivities in terms of molecular flow, using boundary driven non-equilibrium molecular dynamics (BD-NEMD). Transport diffusivities are also independently calculated using equilibrium and external force non-equilibrium molecular dynamics (EF-NEMD) simulations, after accounting for the adsorption on the pores. We show consistency between the approaches for quantifying transport in terms of permeabilities (Darcy flows) and transport diffusivities. We find that smooth slit carbon pore models, which are commonly employed in literature as surrogates for kerogen regions in shale, are an inadequate representation of ultra-confined natural pores. For slit pores, the flow patterns are characterized by a fully-mutualized plug-like flow and fast transport. However, by incorporating even a small amount of rugosity (roughness) to the solid walls, the diffusion coefficients decrease dramatically with surface roughness significantly affecting the characteristic transport and velocity profiles inside the pores. In all cases, it is seen that there are important cross-correlation effects, influencing the way components of the mixture flow together. Calculated self-diffusivities are orders of magnitude smaller than the observed transport diffusivities for liquid mixtures. This work has a direct impact on the understanding and modelling of unconventional hydrocarbon recovery and flow in organic shale rocks.