So we all agree that the science senpai is a time looped Misaki, right?
I mean, they even make misaki do his hair in a similar fashion the next chapter.
Also, I agree with Macrosis and others about the gal game mechanics undermining the narrative, it could be redeemed somewhat if I'm right, though. Given we've been given clues that the game will reset if none of the heroines are won over by the game protagonist, I suggest that the intrigue will progressively move towards time loop stuff. Given that the (manga's) protagonist is Misaki, it would make sense for an alternate version that came to fall for Hareta to try to break the game from within. This would give an interest for the video game rules they all abide to. Though it doesn't really adress the lack of impact if none of the characters are "real". I guess we'll have to wait and find out.
I'm pretty sure about the senpai, though.