The BOS can moderate the raw internal marks submitted by the school by comparing the aligned exam marks. If the school is sending in real high raw internal marks, but that cohort does poorly, this will be reflected in their moderated internal marks, even if they did well all year. It would be assumed the school set really easy tests, or marked easy.
Therefore your HSC exam result, (and your schools) techinically has a higher weighting than the internal mark.