The Bais Din takes nothing into account here except whether or not the child fits the criteria to be poskined a BSuM. His din is already established specifically in the Torah. The Bais Din is taking nothing into account except whether or not the criteria for BSuM have been met. They are not deciding a punishment.
Why did the Torah poskin skilah?
What I am postulating is that, per the Gur Aryeh’s understanding, the reason that the Torah poskin’s skilah, is because the Torah is taking into account the BSuM’s future behavior and punishing him for that future behavior now.