VCAA has not provided information about how SACs will be standardised - in addition to their normal processes - due to remote learning. (I think that's because this was a thought bubble from the education department to give the impression that they were looking out for students, but they hadn't really worked out the details.)
You should not assume that just because you did well in an on-site SAC but poorly in a remote SAC, that your ranking will only reflect your score from the on-site SAC. You will need to demonstrate that you were unfairly disadvantaged by remote learning; I suspect that performing poorly on a SAC is not sufficient evidence.
As to what your school has said, this can be a self-fulfilling prophecy, because your school could simply adjust their ranking to reflect the scores from on-site SACs. While this could be rationalised as compensating for any disadvantage caused by remote learning, it also penalises students who performed poorly on the on-site SAC and worked hard to perform better on the remote SAC.