So Yami admits to herself that she still has feelings for Yuu and wants to run into his arms.
You're saying this like it's some sort of revelation. But we already knew since long ago, 13.5 has her lamenting the fate that it just had to be Yuu who Hikari fell in love with.
So, she's angry that the first thing Yuu does is mention Hikari.
That's only natural, they haven't seen each other for a year and it's an absolutely dramatic and thrilling moment for her, yet his first words are about Hikari not being there. She is frustrated by the discrepancy between her own emotions and his attitude.
She gets mad again when the topic of Hikari comes up.
Where? She brings her up herself.
She gets mad when Yuu doesn't want to talk about Hikari. She's getting mad at the thought that she thinks Yuu expects her to root for him and Hikari when he hasn't even said anything about that. She's making up reasons in her head to get angry when just one chapter ago she was telling herself that Hikari was going to confess to Yuu and it would turn out well. Seems to me like she's not buying what she's trying to sell.
Basically see above. It's a mix of him not reading between the lines (hence "Do you seriously think I don’t care anymore?") and his attitude. She is making up reasons a little, but it's not because she wants to get angry, but because of the overall frustration that he just kept accepting her lies and replying accordingly, as if she actually was just a girl who simply got bored of him and asked about Hikari just for fun.
She internalizes that Yuu hasn't done anything wrong but just previously she was talking about how what she's feeling and what she's saying are out of sync. While she hasn't said anything about that topic yet, you could infer that if her feelings and words are out of sync then her thought that Yuu hasn't done anything wrong would imply that actually he has but she hasn't said that yet.
I am completely missing the logic here. If what she's thinking and what she's saying are out of sync, why is your conclusion that her thoughts must be false? I can follow up on further points when you say her thoughts might not be real, but first explain the logic please.
Yuu's doing what Yami asked but she's pissed off that he would "dare" to say "see you" when she's trying to cut him out of her life completely to make things easier for Hikari. She's also mad that Yuu's walking away. I mentioned earlier that Yami thought Yuu always lets go at the most important moments and here he is doing it again.
Again, see above. He's accepted every convenient lie she told him (which were all actually hurtful for her) without ever challenging them, but he still said and showed he cared about her. That's why she calls it a beautiful memory later, she is still dear to him but challenging her lies means complications, so it's easier to leave it just as a memory. All the while she is there, trembling with excitement of seeing her beloved one for the first time in a while.
Right at the end she mentions that even though Yuu had walked away, now he was right in front of her again. Even though Yami admits she's hitting him with a messed up grudge it still allowed her to get him to come back instead of immediately going to Hikari.
Are you actually implying this is a manipulation? I mean, she is having an emotional outburst, pouring out her feelings on him all the while questioning her own words, and you think this is all intentional just to prevent him from going to Hikari? This is just too Hikari-centric if you ask me. Like, she is laying her feelings bare before the boy she loves, and you think there is actually some friend on her mind at that moment? Just ridiculous.
Why did she go back? I think part of her deep down felt there was a chance she'd run into Yuu if she went to the classroom and since self-destruction is part of Yami's kit she went that route.
Again, what self-destruction? There's naturally a part of her who wants to see him because she is still in love. Not for some dubious purpose like self-destruction, she wants to see the boy she loves, simple as.
Here we get some damning information. Yami, being the one to ghost Yuu, knowingly points out that Yuu didn't say goodbye last year.
I believe this is a mistranslation.
She goes
「そういえば、一年前は言ってなかったよね……」
-snip-
「さよなら、夕」
There is no subject in the first sentence, but in such cases the speaker is usually the subject, at least without context from previous sentences. So basically she is saying she didn't say goodbye last year. And then continues with the actual farewell. It's not about Yuu not saying goodbye, it's about herself.
And his remark about being cowardly is left ambiguous. It could very well be about all the unfair words she said to him, but my bet is that he refers to saying goodbye immediately after having her outburst and kissing him, that she's now doing more or less what he intended to do before - leave without further heart-to-heart, but after causing the damage already.
I would stipulate that Yami kissing Yuu while knowing that Hikari was watching was not only an action taken to sabotage Hikari in her confession to Yuu but also an action taken to sabotage Yuu in his acceptance of Hikari's confession
Or it could be just a girl kissing the boy she loves in the heat of the moment.