I was also a bit confused by senpai "realizing what she wanted as thanks". Because of course she absolutely knew that the blonde wanted to be with her, so it must be something else. So my best guess is that the blonde wanted senpai to at least change, perhaps on her behalf specifically. After that incident the blonde takes a hit for senpai, she internally laments that afterwards absolutely nothing changed about senpai's behavior, or their relationship. It's not until much later that senpai reflects and literally takes a look at herself in the mirror. After changing, she sees herself unblemished by hickies & bruises, feels liberated for once, and finally understands what the blonde wanted. Just like the title implies, the blonde made her own mark on senpai, both literally with the hickey before leaving forever, and more importantly, figuratively with her permanent departure from senpai's life.
I disagree on what she wanted, I think it was less about changing and more about the "on her behalf". The blonde hated how if she died the black haired girl would move on immediately, and that she hadn't left a permanent mark on her life. So by ghosting her like this she left a mark on her much stronger than any of the hickies recieved, or to put it in meme terms she "lives rent free in her head" now.