Yeah I wouldn't argue that he is a main character. Same logic could be applied to any of the girls who the MC currently CLEARLY has an attraction to. Chika isn't one of those.. yet.
However while the two of them appearing in the flashback does make it confusing, Yuka says in one of the post chapter "set scenes" that there isn't any incest.
Yet she was in the flashback. Important, not a love interest. Your bond as siblings probably grows quite a bit though. Not sure what that means but either way, that aside..
Obviously it's not the same situation with Chika. I just think it is way to early for people to be developing that kind of connection to Chika. I mean obviously eventually she'll be up for a relationship but at this point of the story? Not sure how anyone would even think about going for her "route" and getting upset about something that is clearly a temporary arrangement in the game. That's like getting upset about your gf having had fwbs before you got into a relationship. Makes no sense.
That's why I don't understand how it is NTR.