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.
I understand this Patreon issue. And maybe it's just me. As a proverb from my country says: "looking for hair in eggs". Since I see this kind of "censorship" as absurd. Even more so because I follow around 20 works here and it was the first time I saw something similar. Well, whatever. I'll try to follow the story as far as I can.
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