Then it has no legitimate say over the affairs of Gaza.

An Israeli court can say what it wants, but can't have it both ways.

That's nonsense.

The supreme court has jurisdiction over actions taken by the Isreali government, regardless of where those actions take place.

It adjudicates the actions taken by all Israelis. Its jurisdiction should stop at the border it recognises. But it continues however to award land outside Israeli territory to Israeli citizens by ruling on the status of settlements. That is extra-territoriality.