I feel like I didn't read the same comic as some of the people commenting here??
The reason her work is not accepted is outlined in the very first page. Kei is extremely uncharismatic and her work has huge ethical concerns. The latter part is what this entire comic is about. Granted her presentation didn't necessarily involve the romance code, but sentient customizable AI is pretty inherently rough territory.
She gives a breakup speech to a mere robot because she is human and did see Marie as a lover on some level. She questions herself after the fact why she didn't just cut that step out. It's not like the author just forgot she could do that.
I also really don't feel like the comic "suddenly got dark". The setup should be very unnerving if you think about it for even a second. The twist seemed pretty inevitable and like an appropriate exploration of the dynamic to me.
You’re absolutely right. But the visuals of that opening sequence immediately position the MC to arouse the sympathy of the reader—she’s young, wide-eyed, and under duress, while the people she’s talking to, at first unseen, are revealed to be a group of literally faceless bureaucrats who won’t even let her finish speaking. And the ethics concerns are not even first on the list of their objections.
So I agree that the setup should be unsettling if you think about its implications, but the way it’s presented seems to be designed for us to not think about that very much as we focus on learning who this MC is and what she’s about.
From what I know of this author’s other works, I suspect that discrepancy is intentionally part of the story’s narrative dynamic rather than an accidental double message. But it’s only a feeling of mine.