Ayame wanted a seal to protect her son's eyes from the enemy. Meaning the seal is currently on the eyes of Seigetsu. One of the Rinnegan would indeed be sought out my many. Eyes wielded by previous "god-like" shinobi without a doubt would be sought out, and as a mother, Ayame wanted to protect her son. After activating the Transcription Seal: Shinra Tensei, to get a big gap between the user, and the opponent, the users crown (head) is wrapped in a type of sealing bandages, that can not be undone at all, except by the user of the jutsu. Ayame stated that nothing can penetrate the bandages, not even the power of Sannoto's senjutsu enhanced metal. For extra security, the seal also blocks all flow of chakra into the Rinnegan.