I was ranked 2nd in 4u maths and behind 1st by 0.5%.
I got the highest external with 98 but got an internal of 95 because the cohort did quite bad in the hsc exam.
So to answer your question, yes, the system can be quite unfair.
It is fair. At school, you were probably reasonably close to each other. In the exam, the tail did quite bad and stretch a seemingly close cohort, which affected your mark. Whilst you may blame the system, it is really your school's assessment and your cohort which are at "fault", if any can be given. If you got the highest HSC exam mark, you should have really came first at school. The assessments may have been too easy or not effective enough to clearly distinguish you from the student ranked 1. They may have been too easy in that the majority of the cohort were reasonably close to you and their marks were reasonably spread out.
This isn't unfair because the process of moderation reflects your performance relative to the state. Your school mark, where you were 0.5% behind first place, is your performance relative to your cohort. Essentially, if you were able to achieve 98, and the rest of your cohort did average, then it shows your school assessments were far too easy or not effective enough. (or the other case is that the information you have about your marks and others are inaccurate)
Your situation is nothing like the OP, from the limited information you have given and know.
So really, the system only accommodates the <(200-150) schools?
No... forget about these rankings. They aren't official. The have no bearing on your marks. The system is designed to determine your marks which are relative to your cohort and transpose that to marks which are relative to the state. It works reasonably well, and the logic is fair for students as a whole.
BOS doesn't think, "oh, you're in a 400's ranked school, so let's give you shit marks". No, they don't do that. If everyone in your cohort achieved HSC exam marks ranging from 99 down to 90, then ALL moderated assessment marks will range from 99 down to 90. They pin the highest and lowest exam marks, and those marks will generally be the moderated assessment marks of the first and last ranked students. Then the marks are determined by a process of moderation whereby essentially, the more raw schools marks you have, the closer you are to first. They don't go by rank. BOS compares the mean of your school marks with the mean of the exam marks, and adjusts it accordingly such that they accurately reflect your school performance as if you had sat the exact same school assessments as everyone else. That is the idea of moderation. No where does your overall school rank (even though they are inaccurate) come into consideration nor does your individual rank, except if you are first or last.