Actually, it can't be her either since the doll outside the mausoleum is a catgirl and mentions that Masha looked exactly like her, and she has different hair and distinctly a tail, much like Semet.
The memories in the apple pie chest are a dead giveaway she's proto though, especially since she mentions failing to die, burying burning hatred and suspicion away and the fairy that wanted the apple pie mentions cooking is also closely related to proto. plus the small pot that used to be her is eternally emitting heat, which alonside fire is closely related to her too. It's very likely that what you fight in the mansion are both the power and the regrets she mentioned lost after her apparent death, so Rachel's the real Proto and the one you fight is very likely what remains of her when she used to be one of the Saints, which also explains why she's just playing a supportive role given she doesn't have any power to fight with anymore.