It seems like... Shiho (dark hair) and Emika (light hair) began having sex as friends, after knowing each other for a long time. At some point, before or after, Shiho started to feel attracted to Emika, but she becomes increasingly uncomfortable about the idea of doing all these things in the absence of mutual love or a romantic relationship, while also falling into a loop of internalised homophobia and denial. The story begins, and Shiho starts thinking about how she kinda gets taken for granted by her seemingly innocent friend.

Emiko talks about how they only ever kiss when they're already having sex, and that she likes the "funny faces" Shiho makes after they do. They kiss, and Shiho gets turned on, but when she touches Emiko, she realises that she "isn't wet", which I think is supposed to be a red flag about the difference between their feelings: Shiho is aroused just after sitting on the same bed with Emiko and making out a little, but Emiko doesn't seem to feel the same sense of excitement or urgency. Dwelling on this, she starts getting mixed up in damaging thoughts about how it's too difficult for two women to be a couple, that they can't be honest about their feelings for each other because life would inevitably drive them apart, but they could always be together if they stayed friends.

With this conclusion, she decides that it would be better to lock their relationship at that level, and stop putting it at risk by having sex; however, upon hearing this, Emika enigmatically asks what Shiho thinks the difference is between "having a friend to have sex with, and having sex with a friend?" In other words, it's implied that for Emika, at least part of the reason she's friends with Shiho at all is to have sex with her, and that it had never been about love in the first place. Suddenly confronted by the yawning chasm between their feelings, Shiho's expression turns cold, and it's revealed that this is exactly the "funny face" Emiko always loves seeing. While Emiko had never been in love with Shiho, she was very much aware of Shiho's feelings for her; all along, she hadn't been naively taking Shiho for granted, she had been actively pushing the limits of how much bad treatment Shiho would put up with out of love. Whenever they kissed, Shiho's feelings of pain and loneliness would show on her face, and it was that feeling of power, of being loved so desperately, of being able to put someone through so much pain and still have them follow her around like a loyal dog, that turned Emiko on the most.

As Shiho grapples with the idea that Emiko might simply discard her if they stop having sex, her expression of shock gets Emiko in the mood again, and the story ends. Whether Shiho breaks away from her childhood friend, heartbroken and disillusioned, or if she is trapped by love and despair as Emiko's plaything, doomed to be twisted up and pushed around until Emiko inevitably loses interest and throws her away, we never know.

I can basically agree with you up until the line where Emiko says, "What's the difference between having a friend to have sex with and having a sex friend?" because I believe it wasn't her intention to hurt Shiori, but rather it showed Emiko's naivety to the ways of the world which was emphasized in the beginning of the story, and that she only sees being in a relationship as "having a friend to have sex with". So she was asking what's the difference between what they have know and what it would be like if they were dating, and thus the look on Shiori's face in the next panel isn't an expression of shock from terror, but rather from happiness or embarrassment, and that's the face that Emiko likes to see.

Then there's also ambiguous things like on page 107, where after Shiori brings up the topic of love, right before they kiss on a close up of their lips one of them begins to say something that beings with I love before getting interrupted. We can assume that it's Emiko though, since as long as we follow the 180 degree rule, it was the person on the left with her lips open, which Emiko has been.
All in all, if you read into it a bit, it's not really a story filled with angst, and I agree with it not being tagged us such, but just a light-hearted one off.