Putting this cross-posting this and on Discord and Tumblr because this is so intriguing
Shion and the snake imagery isn't too new in No.6 meta or casual posts, which is why I want to see the snake skin shedding metaphor as a division between two Shions: the perfect Shion and the imperfect Shion, and tying this to the self-contempt Shion had in the original Nine novels (double identity Shion dojhwoidv)
Original 9 suggested that from Safu, before Shion, the brown hair Shion had so many expectations and awards that things were being planned for him in the educational program. Even as he was removed from the program, Shion from before still got a job that he can sustain for quite a while. The Shion from within the walls was 'perfect' -- a highly intelligent person who had backup plans over backup plans when things are not right. The Shion as an identity crafted by No.6 itelf and holds the 'perfection' indifference of his.
Meanwhile, the Shion that survived the West Block and searched through the Correctional Facility, the Shion that reached out to Nezumi - the Shion who is conflicted and re-awaken is 'imperfect' - the person work for a new identity and the person who is more emotionally driven and hated -- really hated himself -- bit his tongue in frustration and disbelief of himself.
What separates them is the 'illusion' that was partially crafted by No.6. When Shion said that he isn't as truthful as Nezumi or Safu, I think this is what it is - the perfection in Shion is all a lie (or at least that's what he thinks, and its partially right via ignorance of the world outside). As the 'walls' within Shion breaks, Nezumi is one of the only people he can trust because that is what he's left of the world that lied to him.
Thinking back to the thought that there's a jarring voice that tells Shion he is weak, and that if he is going to leave Nezumi to save himself. I think that is 'Perfect Shion's voice - is that kind of twisted No.6 narrative that influences this thought - the narration of 'individualistic success', 'finding reason above all' kind of thought from Perfect Shion to Imperfect Shion
In Beyond and later Reunion, I think 'Imperfect Shion' is working through the scraps of 'Perfect Shion' - that indifference and more interrogative nature of the Shion who is built to think in highly bureaucratic and demanding nature - but also with the critical understanding, experience of Imperfect Shion - then it is Shion trying to figure himself out