In order to characterize giant exoplanets and better understand their origin, knowledge of how the planet's composition depends on its mass and stellar environment is required. In this work, we simulate the thermal evolution of gaseous planets and explore how various common model assumptions such as different equations of state, opacities, and heavy-element distributions affect the inferred radius and metallicity. We examine how the theoretical uncertainties translate into uncertainties in the inferred planetary radius and bulk metallicity. While we confirm the mass–metallicity trend previously reported in the literature, this correlation disappears when removing a 20 M ⊕ heavy-element core from all the planets. We also show that using an updated hydrogen–helium equation of state leads to more compact planets. As a result, we present six planets that should be classified as inflated warm Jupiters. We next demonstrate that including the opacity enhancement due to metal-rich envelopes of irradiated planets changes the planetary radius significantly, which can have large effects on the inferred metallicity. Even though there are other model assumptions that have not been considered in this work, we could show that the calculated theoretical uncertainties can already be comparable or even larger than the observational ones. Therefore, theoretical uncertainties are likely to be even larger. We therefore conclude that progress in theoretical models of giant planets is essential in order to take full advantage of current and future exoplanetary data.