actually it working correctly. the problem is the bones were not connected. if you are using blender and rigify, if the bones are not directly connected then you have to set a “rig type” for the bone while in pose mode and then for the constraint you have to type in its parent bone deformation. only when you do this will godot still connect them in the skeleton on export
My workflow now uses this, GitHub - catprisbrey/Rigodotify: Rigify to Unreal/Unity/Godot GameDev Armature converter · GitHub , you still need to set the rig type when adding more bones to it but it will reorganize the bone structure so everything is a child of root now so you can use root motion.
