Basically, the bodies are just definitions that you need to match up to the skeleton (mostly.manually) and seemingly are created automatically based on weight paint.
the constraints cannot overwrite the skeleton joints. They work with them regardless of where they are positioned.
The limit the rotation, and twist of the joint according to how you set up the constraint.
There is no retargeting happening. Its just a specification that alters how skeletal meshes react to physics influences.
The phat asset doesn’t really deal with the weight paint (other than possibly deriving capsule size from jt).