One thing it's on my mind now, did Makoto knew Yukari was related to the person responsible for his parents death from the beginning? Cause now that I think about it there is a huge possibility he did after learning her name.
Considering how Yukari talks that she and her mom had to move many times and even moved to kyoto due to people being very mean to them this kinda shows the information of who they were was public, and very possible he heard people around him talking about Yukari's dad.
And then when he wakes up after awakening his persona she doesn't give many details but she says her father worked for the kirijo group and he was the chief researcher, his name was probably all over the news. Even if Makoto was a kid it's very possible he researched or just listened someone saying something. So he could have put 1 and 1 together.
Same way, Yukari says she knows his story. In the movies mitsuru handles his file to Yukari and she learns it from there. But it's very possible Yukari already knew a boy lost his family from the news, even if she doesn't it would still hit her learning his past.
So imagine how it was for her listening many times her father was the one responsible for what happened, then she meets this boy who lost his family because of her father's actions and then she sees him sleeping through a whole week because of her inaction. No wonder she just starts talking to him the moment he wakes up.
Now imagine Yakushima beach scene. Where everyone learns that he was responsible for releasing the shadows. How Makoto felt there learning this? And yet still comforts Yukari. Like he may have already come to terms with his loss, but considering his situation he could have handled everything very differently, and yet he tells Yukari to continue believing in her father, even when all evidence points otherwise.
Their stories are tied in such a way that they are on both sides of the incident, and they parallel each other.