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 didn't find a good place to insert this above, but I do like how it's not until senpai is free of bodily marks that the mark the blonde left is apparent, paradoxically.
I enjoyed this story, not only because of it's introspective & melancholic slant, but the fact that it ends hopeful like Koveras explained very well above. Most stories like this end up with characters never growing for the better and remaining trapped in their toxic circumstances, which never personally sat too well with me, even if that was the purpose.
I think this chapter stands well on its own, and I wouldn't be dissatisfied if it ended here. I'm mainly worried the second part of the twoshot will involve a relapse with the blonde and end pessimistically, invalidating the message of this first chapter. But after this chapter I'm confident the author will deliver quality like this.