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Low-metallicity dwarf galaxies often show no or little CO emission, despite the intense star formation observed in local samples. Both simulations and resolved observations indicate that molecular gas in low-metallicity galaxies may reside in small dense clumps, surrounded by a substantial amount of more diffuse gas, not traced by CO. Constraining the relative importance of CO-bright versus CO-dark H2 star-forming reservoirs is crucial to understand how star formation proceeds at low metallicity. We put to the test classically used single component radiative transfer models and compare their results to those obtained assuming an increasingly complex structure of the interstellar gas, mimicking an inhomogeneous distribution of clouds with various physical properties. We compute representative models of the interstellar medium as combinations of several gas components, each with a specific set of physical parameters. We introduce physically-motivated models assuming power-law distributions for the density, ionization parameter, and the depth of molecular clouds. We confirm the presence of a predominantly CO-dark molecular reservoir in low-metallicity galaxies. The predicted total H2 mass is best traced by [C II]158um and, to a lesser extent, by [CI] 609um, rather than by CO(1-0). We examine the CO-to-H2 conversion factor vs. metallicity relation and find that its dispersion increases significantly when different geometries of the gas are considered. We define a clumpiness parameter that anti-correlates with [CII]/CO and explains the dispersion of the CO-to-H2 conversion factor vs. metallicity relation. We find that low-metallicity galaxies with high clumpiness may have CO-to-H2 conversion factor as low as the Galactic value. We identify the clumpiness of molecular gas as a key parameter to understand variations of geometry-sensitive quantities, such as CO-to-H2 conversion factor., Comment: Submitted to A&A, comments welcome