As I understand it, they're the analogue of thumbs/big toe. Think about your middle finger in relation to your thumb. There are several joints on the finger corresponding to the fetlock and the bones in the foot. Then the thumb joins the hand, and then you get to the carpal joint (your wrist/the horse's fore-knee). So that's why, I think, the vestigial "thumb" is just below the carpal joint.
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