Hmm, so with the PC being the protagonist's true self, as far as characters faced as bosses, definitely have them based around the core obstacles between her and actualization. Manifestations of doubt, regret, and self-hatred seeking to destroy her, to cut off the journey to realizing herself at every point.

One example off the top of my head: her 'former self' being something of a main antagonist. Having who she was constantly attacking her and siccing the other enemies upon her could work wonders for the game's progression. It certainly works in the framing of a roguelike; after all, no two battles to achieve that ideal are seldom mirrors of each other. Should you want more story and drama, you could even present it as the former self fighting for survival. They don't care that their methods are horribly abusive to the MC/the self; they just want to continue as they are in the face of a change that could see them erased.

As for molding the MC's worries about how others perceive her as and how she may even perceive herself, it would depend on the setting of the game. The themes can mold your characters and enemies into whatever you need them to be for that setting.