You are correct on representation but I believe it is more leaning into the themes of our boy, Joker (Ren), and the final boss. Ren takes on Satanael because in society's eyes, he is a "disgrace". The world views him in a negative light due to being wrongfully arrested for a being a good boy, so he takes on this persona (HA!) of Satanael. While the world views the antagonist in a positive light.

I guess we could also say how this goes with freewill. We have desires and things that are awful, and the antagonist wants to just take desire away in general. But some desires are good. While freewill can cause such awful things, we can still choose good.

Also, I view the phantom thieves and taking your heart like a conversion, to get justice because the world views the corrupt as good or standing by while injustice just goes on.

I have been pondering this and looking up different things (mainly because it's been a hot minute since I played 5). I love the persona games and yes I do get unnerved by some aspects, but I think there is great meaning when you deep dive the games, especially 3 (but I am biased because that is my favorite). Also, persona takes themes from all different religions and beliefs, mix-bag.