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Very late answer, but if you're still interested in that: 

You need to gather all 12 clues, and then the option to take them to the interrogation room will appear when you talk to them. It's there that you'll make use of all the clues acquired. 

Also totally agree on the MC's disposition to mean behaviour. Most of it is optional  (like, you don't really have to blackmail the nuns, for instance), but there's a lot of content that is gated behind being a bordeline rapist, unfortunately.

But I just love everything else way too much to drop it, haha.

I would like to know that as well. 

I was really looking forward to see a positive relationship between her and the MC. 

Had an ex with that same resting bitch face issues, so I related a lot to her. Really wanted a happier outcome. :/

Either way, just hope we'll get the good karma route someday, or at least an answer as to whether we should expect it or not. Gonna keep her quest on hold until then.

I totally agree with you. The editable relationships were the best way the devs managed to come up with as a workaround that still allowed players to fill either the original roles or maybe something they were more comfortable with, even if some dialogues could become weird. 

You'll only find those in content related to incest, so it's totally and completely possible to follow lots of works here on itch and still be your first time seeing it. The important part is that you're now aware of what it means when you come across it again, lol.

And it's possible that we may be from the same country, haha. Both the proverb and the legality of incest as long as consented and between adults fits the bill. xD 

This trend of using the editable relationships "roommates", "landlady" etc is to avoid the Patreon ban on incest related content, and you'll come across it in plenty of other VNs around here. Whenever you see it, be fully aware that the "original" relationship is that of a blood related family. The inconsistency you felt is probably because of a lack of familiarity with this whole deal. 

Sky is a 100% MC's sister, not only half or just a cousin. 

My best wishes to Jestur as well. Not aware of what kind of problem life has thrown at him, but I hope he manages to get through it and rise back even stronger than before. 

We're all cheering for you, mate!