But wouldn't it just affect your ranking at school?
BOS doesn't look at your ranks by itself. They look at your raw marks, and where you sit in your cohort (not in terms of rank, but in terms of how many marks you differ from the person ranked above and below you).
It may or may not affect your rank, but it will definitely impact your raw mark. Coming say 5th by 2 raw marks puts you in a far better position that coming 5th by 20 raw marks. But you're still ranked 5th, so your rank really means nothing. It doesn't really show how you positioned in your cohort, whether you're a top student or a not-so-good student. If the top 9 ranks differ by 1%, then rank 10 differs by 30%, then saying you're top 10 means nothing...you're way behind the top students in the cohort.
So yes, it can affect your HSC mark considerably. It can be the difference between a Band 5 and Band 6. But at the same time, it may be negligible. It will depend on how you and your cohort performs in the HSC exams.