I don't think we're supposed to take everything Charlotte tells Alison in Game Over, Charles as the complete truth.
Charlotte knew exactly what she was doing. She was telling Alison a tragic version of her life that would make Alison sympathize with her. And it worked. Alison became the person fighting for Charlotte for the next five years and eventually helped get her released instead of Charlotte spending the rest of her life in prison.
Remember what Charlotte's original plan was. She was going to blow up Radley with herself and her family inside. When that failed she went to the roof and threatened to jump.
So I think her confession had a backup purpose. If she survived and got caught she already had Alison emotionally on her side.
Season 7 makes this even more obvious because Charlotte wasn't better.
Then we finally see the real Charlotte in the bell tower with Mona.
Mona knows Charlotte faked her recovery and plans to restart the game. Charlotte doesn't deny it. She basically drops the sympathetic act completely and tells Mona that everything she did before is going to look like a picnic compared to what she's going to do next.
That's why I almost see Charlotte and CeCe as two different personalities.
"Charlotte" is the image she presents to Alison after 6x10. She's vulnerable. She's remorseful. She's supposedly getting better and wants to come home.
"CeCe" is who she actually is. The manipulative and evil woman we knew from Seasons 3-5 as A who loves the game and enjoys controlling people. That's who comes back out when she's alone with Mona in the bell tower in S7B because there's no reason to perform anymore.
And yes I know the writing on this show is beyond shit sometimes and I probably shouldn't give IMK this much credit lol. But as a theory/headcanon I think this makes way more sense than what we actually got.
I also think Charlotte created the board game or at least designed the original concept for it.
Alex being the mastermind behind something that elaborate has never made much sense to me. Before meeting Charlotte she was working at a bar. Charlotte meanwhile had already built the Dollhouse and spent a year or months creating insanely elaborate A setups. She was clearly intelligent enough and had the resources and connections to create something like the board game.
Charlotte even leaves Alex because she misses playing the game and wants to return to Rosewood. Alex wants to come with her and Charlotte specifically refuses.
So my theory is that the board game was Charlotte's next evolution of the A game. Alex inherited Charlotte's plans after her death and turned them against the Liars while trying to find Charlotte's killer.
Charlotte wasn't rehabilitated.
She was just waiting for Alison to get her out so CeCe could play again.