jailkit_chroot_authorized_keys_template in shelluser_base_plugin.inc.php
There are two shelluser_*_plugin.inc.php files, shelluser_jailkit_plugin.inc.php was updated to use the jailkit_chroot_authorized_keys_template server config setting, but shelluser_base_plugin.inc.php still has /root/.ssh/authorized_keys hardcoded. I have not explored the conditions under which the latter is effective (I'd guess creating a shell user which is not using jailkit?).