Just because a lower court finds something illegal, doesn't mean that it is illegal until the final appeal.
Actually, it is “illegal” unless and until the higher court overturns the lower court’s decision. What do you think the position would have been if the High Court had refused Qantas leave to appeal? The majority of judicial decisions are not appealed to any higher court and the great majority of applications for leave to appeal a decision to the High Court are refused. (Some stats on applications to the:
High Court.)
A higher court can effectively delay the operation of a lower court decision, pending the outcome of an appeal, but I think that’s a matter of discretion in most if not all cases. Are you aware of any authority for the proposition that the grant of leave to appeal to the High Court ‘automatically’ stays the effect of the decision appealed against? I may have missed something.
But, as you say, the High Court could ultimately find that the Federal Court got it wrong.