It's blackmail and pleasure corruption... what are you on about?
It's not confused about anything at all. Kana doesn't have much of a choice, and depending on triggered events, she can lose her virginity to L pretty fast. (Generally by Kana ending up drunk.) In case you didn't notice, L isn't entirely content to
just fuck Kana. He explicitly wants to make her submit to him, which is why he plays along with her resistance, when he's not made extra angry anyway. Kana's naturally more resistant during the day and has less excuses during the night, so the night scenes are more intense from the start.
It's also NTR, y'know, the genre where sex has similar effects to hard drugs? The submission score is related to that, showcasing Kana's lowering resistance until she just snaps and sex becomes her number 1 priority.
I agree that the way it works in the day-time is not ideal, but that's partly because the game was never optimized beyond initial playthrough status of the intended path. If you play things straight, in the 1st playthrough, you're not gonna have enough hi-rez cameras, and enough cameras in general, to keep track of what Kana's doing. You'll be relying on phone calling her or clearing things properly to stop L from messing with her. So MC not having better reactions to things won't really be a factor in the 1st playthrough unless you're explicitly trying to cheat and/or farm for scenes from the get-go... in which case it's on you.
And of course things break in NG+, d'oh. That's pretty normal for NG+.
It obviously doesn't help that BBQ clearly wanted to have a path where the MC enjoys watching Kana dicking around. It's why we have the so called Netorase ending to begin with after all. So the current situation isn't quite as bad as I've seen in some other NTR games where the MC is just a complete dumbass. In this one at least you can think that he's conflicted about things.
That said...
You're not even that guy... Maybe his opinion on why it misses the mark is entirely different from yours.