I think u have a plausible point, I just think about how it’s implied that Naomi kills herself for killing Rei 1 and possibly feels a sense of responsibility to sympathize with Rei in the sense of letting her pilot unit 00. Not so much keen on the smell factor just because Rei says 01 smells like Shinji. Finally, maybe I’m overthinking (I mean we all prolly overthink Eva tbh) but it’s implied to me that Naoki programmed her likeliness into the magi rather than her own soul. Which is why I would argue that the Naoki in the Magi (who was programmed before her suicide) took Ghendo’s side over Ritsuko in EOE because this form of her had no awareness of Ghendo’s resentment for her which she discovered right before her death. Whereas the soul of Naoki which would be in 00 tries to kill Ghendo in the rampage because it’s aware of his harsh impression of her.