I’m no lawyer, but I thought most federal cases were handled in state courts anyway. Import drugs into Australia (federal offence) and get caught in NSW, then you would face court in NSW and go to jail there. Doesn’t really matter if a federal or state offence, consequences are the same.
Im not sure if there has been anything enacted (health order wise) federally (regulated by CASA) regarding masks on domestic flights, so maybe you only face whatever state rules you bust. Maybe disobeying a crew order, as a federal offence (crimes aviation act) and you would end up in court wherever you land.
If you committed an offence by not wearing a mask whilst flying over NSW, then I guess you could be summoned to a NSW court to face the law.