In this research, we rekindle an old debate by questioning the impact on mitigating policy evaluation of detailing a subsector in a global energy-transportation model. We chose the refining sector because it is a relevant case of a sector for which representation widely differs across models and because it offers a unique set of complex joint production in the energy sector. To investigate whether the level of detail in the description of the refinery impacts optimal mitigation options, we take the example of a long-term, national, linear programming based, energy-transport system model (TIMES based). We found that the refinery description used in the energy system model matters when trying to evaluate energy or climate policy applied to the transportation sector. It impacts the policy costs but also the technology trajectories chosen at the optimum. Essentially, the balance between energy efficiency and carbon intensity of transport may be affected by the accuracy of the description of the pivotal refining sector. Consequently, increasing this sector accuracy level should not only be motivated by the wish to gain wider quantitative insights on potential evolution of the energy system but also by the wish to improve the robustness of the model outcomes.