I don't think my school ever had anyone get an ATAR of 99+ prior to my co-hort, the dux at one stage was 94. The dux this year managed to get 99.65 with Maths/Science and I got 99.50 with all humanities subs.
The only disadvantage of going to a badly ranked school is that there's less 'competition' or drive to excel academically, and that can result in either a) you making excuses b) complacency. Also, you might lack the support of effective teaching staff, though this usually isn't the case, as with my school, where the teachers were awesome but unfortunately the students were apathetic.
If your school is actually that shit, then you should be able to come first in every single one of your subjects, it's what I had to do. And this might sound harsh, but if you can't come first in your internals at a school ranked 300+, then 99 would've been out of the question even if you had gone to a well ranked school. So yes, it is HIGHLY possible if you have the natural ability and/or work ethic - come first in all your internal subjects and make sure you're being marked in accordance with accurate HSC marking standards. Good luck!