Plus while the big guy tried to rape Kyou, he didn't take his clothes off, he insta got stabbed with a pen. Half the chapters called Kyou a "she". Would kinda also explain this infatuation of hers for MC, like hers evil alter-ego "experiment fun" sipped into hers "interest in a guy". I don't recall ever seeing them both at the same time, but they kinda were going to different schools and no info about missing days were given, so its still a bit of a stretch theory.
Her plot armour saving her all the time from bad things that borderline kill or break other girls could be explained by this theory, but it could also be explained by her needing to be alive so she could be used to finally break MC if the manga will have a bad end, or save him somehow?