MC being experimented on by his mom seems to be all but completely confirmed already. Several dialogues about his medical results from the school nurse, reported directly to Himmel, showed that MC is definitely not normal. Discussions have mentioned his mom was working on a research project involving genetics that Himmel was also involved in.
It was near the beginning, so details are a bit fuzzy, but I think I remember that MC's mom left Himmel's team and continued her research in secret. With her sudden death, all of her research was thought lost, but Himmel seems to have suspected that she was experimenting on MC, and the "routine medical checkups" at the school seem to be confirming his theory.
It would explain why Himmel has shown such interest in MC, and only after his mom died. Also explains why he sent MC to that school, where the school nurse is in his employ, and required comprehensive medical testing that doesn't appear to be the norm for students there.
As for the new girl, I really didn't notice anything suspicious about her behavior. I don't think she ignored MC at first, but just greeted him last, since she already knew Emilia, and Giulia was gushing over her. I think MC's apparent lack of interest in her probably threw her off a bit, but also probably intrigued her as well.
On the subject of Patreon, the reveal about Megan being super turned on by Sofi being her sister kind of suggests that dev isn't too worried about that particular taboo. A MC/Sofi/Megan threesome seems inevitable in the near future, and if dev were worried about Patreon, he likely wouldn't have made them sisters. I also can't imagine dev not giving us the Aki/Kari threesome at some point, and Patreon has made it clear that a threesome involving family members, even if the family members don't touch/interact with each other, is still a violation.