I reckon that they'll appeal. They have much to lose and keeping out from under another inquiry benefits them*. You can't bet on a court result, generally, so their bet could pay off, should they decide to appeal.
The WT is trying very hard to strain out the gnat of the wording "in care". The royal commission has already decided that the WT is within its ambit. Even if the supreme court sides with the WT, what's to stop Parliament establishing an investigation specifically into CSA as handled by the WT?
I can't imagine the royal commission pussyfooting around, once they have the WT in their clutches. With the precedents from the ARC and Norway, this time around they'll be well informed and know what to look for.
As usual, the WT is playing the "religious freedom" card. Religions are afforded various freedoms by governments, but there is one freedom that they don't have: the freedom to handle and investigate criminal matters and to exclude government police and judicial processes.
*The upper management, of course.