Biological optimization for treatment planning in carbon ion therapy is currently based on the first version of the local effect model (LEM I). Further developments implemented in the latest version (LEM IV) allowed to predict more accurately the Relative Biological Effectiveness (RBE) in-vitro. The main goal of this study is to compare the LEM IV against LEM I under treatment-like conditions for idealized target geometries. Therefore, physical dose distributions resulting from the biological optimization with LEM I were used to recalculate the RBE-weighted dose distribution based on LEM IV. Input parameters representing the clinical endpoints late toxicity in the central nervous system and the tumor control for chordoma were chosen to investigate the impact of changes on the predicted isoeffective dose levels. The recalculated RBE-weighted dose distributions show an increase within the target region, and the mean RBE-weighted dose values are dependent on the geometry and decrease with increasing target dimension. The differences between predictions of LEM IV and LEM I are less than 10% for typical tumor volumes treated in the pilot project at GSI. Median RBE-weighted doses predicted by LEM IV in the target region are consistent with clinically observed dose-response behavior as demonstrated by comparison to the 5-year local control curve for skull base chordoma.