I'm on my first playthrough still in season 1, and man, it would have been nice if there was a Kim path where I don't have to be an asshole but I also don't have to tell her I "love" her skin condition. I have no intention of pursuing a relationship with her because I do not find her attractive, but I also wouldn't be a dick and tell her that she should wear full body makeup all the time to hide her condition/be ashamed of herself. There really should have been a middle ground.
Not to mention that not going all in on her also causes you points with all the other starting students. From what i've read you want everything to be optional, but in this case it seems like you're punishing players for not going totally full harem. It makes it feel like not a choice.
I quote one of your posts, but I will answer every one of your points. I like this kind of feedback, it's discussion-inducing.
That scene is an important plot point for every one of the students, you are telling them that they can be themselves or what "society" expects from them; you are not telling them the MC is in love with (or interested in, or even liking) any of them. That's why it affects differently (RPs change) every one of the girls:
* Kim is obviously the most affected. You are either supporting her or insulting her, so the +10/-30. You are not saying you love her.
* Debbie is as self-conscious about her body as Kim is, so her RPs are the ones that change the most among the other students (+6/-10).
* Kate doesn't give a fuck about the MC's opinion of her, but she hates bullies and she's friendly (and sharing a room) with Kim (+4/-6).
* Lisa is the less affected (+2/-4). She is used to "society" having a say on what she can do or not, and to some people being harsh on her if she doesn't comply with what "society" expects from her.
A lot of interactions early on affect more than one girl, since they talk among themselves (or listen to the conversation) and they decide if the MC is friendly or an asshole. They don't have the advantage of having known him for years (like the closer family and friends including Megan, the Washingtons, and the Lambs) or seeing him act (like Alexia or Maddie). They need to form an opinion of him based on your choices. And they (especially Kate, Debbie, and Lisa) have a previous relationship, so leaning on Lisa will anger Kate, leaning on Debbie will please Lisa, and stopping Lisa's "posh-ness" will please both Debbie and Kate. Kim is the outsider, but she becomes friends with every one of them (or doesn't antagonize any of them, as shown in the conversation in Emma's room).
Note that the negative RPs are higher (in absolute value) than the positive ones. That makes sense since being supportive is "expected" and being a bully isn't. Oh, the irony! The girls don't want to "have to behave" as expected but they judge the MC for how he's expected to interact with them.
The conversation, when supporting her, goes by:
Note the MC isn't flirting with her. He's saying "You could meet
on the campus a new guy". That guy can't be him; she already met him. He said how he would feel if he were that guy (remember the MC has an aversion to lies). He says (being in that guy's shoes) "I love it (being that guy who is already dating Kim), but I would still feel like you lied to me." Kim gets excited about it, asks if he loves it, and it produces a possible misunderstanding (the MC is still in that guy's shoes) because he said something nice about her skin at the lake (he didn't say he loved it at the lake, thus the "I thought"). The MC ends it up with "If I dated someone like you". That doesn't mean he will be dating her.
He's talking in conditional: "If I dated someone like you", "I would still feel like you lied to me", "I know I would feel that way", etc.
Having a middle-ground choice would dilute one of My Dorm's main themes: "You are perfect as you are" (That doesn't mean the MC wants to fuck that perfectness). You can get the maximum RPs with any of the students (the only ones with RPs for obvious reasons) and not start a relationship with any of them. RPs are only about how THEY see the MC (friendly/unfriendly), not about how the player/MC sees them. So you need a minimum amount (+5) to have the chance to open a relationship with them, but you aren't forced to open it.
On a side note, I love how eager some players are to open a relationship with Kim. Mandela effect here. They remember having opened the relationship with her already, and it hasn't happened yet. 
. Losing those points with Lisa/Kate/Debbie isn't relationship-breaking if you are interested in them (if you don't behave like a jerk in the other interactions). Debbie can be somewhere between +44/-26 when the choice to open a relationship is shown, and Lisa +35/-11. Losing 10 or 4 points won't affect that choice showing.
I hope to have answered your points.