Them being different people and able to exist together made no sense to Xion... except that Riku had told her Roxas had to go back to Sora too. So clearly that was also a lie.

"Yes, I see you are awake. I see the proof that Riku lied. Even if you aren't Roxas, if he really is inside you... then destroying Riku is the only way to keep you both safe. You. Roxas. And Axel. I'm done being just another puppet, and I am done being used. I'm choosing. For once I am choosing, and I CHOOSE MY FRIENDS!" she threw her hood back, eyes flaring with fury and determination.