I'm not questioning the reasonings or ethics of the characters actions, or what was going through their heads at the moment, all I'm saying is, that there's more than just one instance of what could be classified as rape, so the tag is fully justified.
And if we go for reasons, yea, MC drugged Yuna to protect Inori, but that doesn't mean he had to have sex with her afterward, the drug is temporary, so the MC could have just left after figuring that Yuna was indeed under its effects and she would be alright, but the MC instead decided to take advantage of her, but that's in line with his character I guess, he's just trying to get any advantages he can whils't been as less of a dickhead as possible.
I don't like sharing BTW, I'm not sure I'll play that route once it comes available if I'm honest, I'm a hoarder by nature.