My best guess without a look at the rig itself is that it’s a humanoid thing since R15 humanoids use rig attachment points to set up the joints on characters. New joints are created on initialization using the attachment points, if present; changing the joints directly doesn’t do anything unless you delete the rig attachments. They’re the attachments suffixed with “RigAttachment” found in each body part.
You can just delete all of them except the RootRigAttachment in the lower torso without any consequence if you’d rather use joints directly. Otherwise you’ll have to position the attachments as desired
There’s a Characters docs page that mentions how joints are made from attachments but it doesn’t get into any specifics. The :BuildRigFromAttachments() humanoid method also touches on it slightly but is similarly vague in specifics