Abstract Modelling the scrape-off layer of a stellarator is challenging due to the complex magnetic 3D geometry. The here presented study analyses simulations of the scrape-off layer (SOL) of the stellarator Wendelstein 7-X (W7-X) using spatially varying diffusion coefficients for the magnetic standard configuration, extending our previous study (Bold et al 2022 Nucl. Fusion 62 106011). Comparing the EMC3-Eirene simulations with experimental observations, an inconsistency between the strike-line width (SLW) and the upstream parameters was observed. While to match the experimental SLW a particle diffusion coefficient D ≈ 0.2 m2 s−1 is needed, D ≈ 1 m2 s−1 is needed to get experimental separatrix temperatures of 50 eV at the given experimental heating power. We asses the impact of physically motivated spatially varying transport coeffients. Agreement with experimental data can be improved, but various differences remain. We show that drifts are expected to help overcome the discrepancies and, thus, the development of SOL transport models including drifts is a necessary next step to study the SOL transport of the W7-X stellarator.