I've been really overthinking, so some working ideas.
Yura with bandages, "bruised and battered": Not pure sadism but Koma's desire to passively look over Yura in an innocent, klutzy form while she's reliant on Koma, without having to take into account the possibility of Koma hurting
Bullying?: Verdict is still out on whether bullying is happening and/or how bad it is, but I would say that it probably is to some degree, in a badmouthing way at the minimum. Potential escalation timeline (in terms of how "undeniable" the proof of bullying is), from 536-39 showcasing Yura's reluctance to talk about school (but possibly just due to not fitting in well), to 543 being a potential push or similar that'd cause a fall onto her face (or just her falling by herself, as happened exactly on 535, and would also mean that she directly lied in 546, which seems unlikely) to 557 with the girls talking about her (clear exclusion), and last, 564 with a wound on her neck that couldn't have been caused by a fall (though also not a common area to target unless the hypothetical bullies were really violent).
The end of the world/the change: Yura's independence and demanding more of Koma, which ends Koma's world as she knows it. Yura, interestingly, is who brings the idea up, after which it's immediately shot down by Koma, but Yura states that she still believes in it. Also an extra layer of Koma continuously denialing the possibility of it, even right before it happens.
The sea: Both a herald of change and Koma's feelings toward Yura which she won't admit, as they would break the normal. Not just her normal, but also the normal. This feels most evident in the scene with the girls from Yura' school, where Koma comes closest to actually doing something on Yura's behalf and "dirtying her hands", as the sea rises, and she wonders why she would even consider it when she doesn't want things to change.
Coward: Koma's inability to join Yura in leaving that world behind and embracing the sea. She couldn't say that having Yura by her side was also all she could ever ask for.
Tl;dr, Rev Girl Utena with more passive, useless lesbian? Still feel like too many pieces don't fully fall into place.