What I got from it is that Koma doesn't want anything to change, including Yura's wounds. She wants her to keep getting hurt because that's a part of the Yura she knows, but at the same time she doesn't want to ask why or what's wrong with her because actually talking about it will change their relationship, it will put her in a position where she will need to take responsibility or do something about it. But she simply wants to meet her every thursday, see her new scrapes and bandages, talk about nothing and go for ice cream. In a way, she fears that if Yura stops getting new wounds, she won't need her anymore. She knows exactly what's happening with Yura, but she denies reality because again, she doesn't want any change. Even if it means wishing for her friend to keep getting abused and hurt. She wishes for it.
When Yura finally decides to talk to her, albeit in a roundabout (though still obvious for the reader and even more for Koma who already knows everything) she just fools herself by taking the lightest interpretation possible:
"She doesn't get along with her class -> she's an introvert so it's expected" when Yura was trying to say she was bullied.
"Someone peeked under her clothes -> a pervert flipped her skirt" when Yura was probably talking about how someone forcefully looked at her scars.
"I want everything to end -> she's talking about the fake end of the world article again" when she was talking about her suicidal thoughts.
And when thinking back on this conversation, she just grinned at the fact that Yura had confided in her and her alone. That she was the one Yura chose to rely on. She's glad, above all, that Yura still completely depends on her, and only her.
Koma is a disgusting coward and Yura clearly knows, probably since the beginning. She knows her situation is obvious to anyone who looks at her, she knows Koma must know too. She test the waters several times to see if Koma will speak up, but every time Koma plays dumb and pretends to take her words at face value, which only serves to confirm Yura's suspicions about Koma not giving a single shit.
The ending was either Yura's plan for a double suicide or a final cry for help where she would confess to everything happening to her directly in a way that Koma couldn't ignore anymore. But she had already ruined their relationship completely by saying she knows Koma doesn't care and looks down on her, effectively exposing Koma for what she is, showing her that playing dumb won't work anymore, and has never worked before. Once at that point there was no going back, but Koma still desperately tried to return things to how they were with her "Let's go home", to pretend nothing happened so they can keep things going unchanged. But Yura was alread on the other side. Koma refuses to acknowledge her, yet again, and the door closes separating them forever.
The sea rising is pictured every time Koma feels anxious that anything might change: when she's wondering how Yura will react at her touching her face and wishes for her to say "it's nothing" as usual, when Yura finally tries to speak to her about her issues (rising even higher after the conversation is done), when the bullies are talking about Yura and the sea covers her feet. This point in particular is important because when she thinks "get out of here already" she doesn't want them to stop because their words are hurting Yura, she's thinking that if they keep talking and mention the bullying directly she won't be able to deny reality anymore, or they might prompt Yura into opening up to her about it, which is the one thing she doesn't want. She doesn't want to hear anything, because that would imply a change in their relationship.
So the seas rise every time anything off-script happens in their weekly meetings that might force her into actually doing something for Yura. The sea first cover her completely when she finally sees Yura without her turtleneck, seeing the deep scars on her skin, and she finally drowns in it when Yura snaps at her for what she really is: a coward.
I think the sea represents her overwhelming guilt she's been trying to brush off for years by pretending everything is fine and Yura is just a klutz who gets hurt on her own, knowingly fooling herself because she knows there's no way the wounds on her face are accidental.
When the consequences of her actions come crashing down, she drowns in her own guilt.