To your last question, yes and no. The fact is, going into this game, it was Harem first and only. It was a story that reinforced the import of the main character. In literature and in almost every other media, there is an understanding of where a character stands and where it will resolve. A trait that tells you the reason they exist. Mom is the forbidden aspect; aunt is the lonely/attention seeking aspect; sister is the naive love aspect; older sis was a love lost aspect. In this respect, this game did this pretty well. There was an very interesting push and pull with MC's mother that kept it interesting and more importantly, REAL. Sure, you were gonna add sharing with MC's friends in school, the brother and sister, but it made sense for this way. I wasn't going to do it, but the option was there and it was fine.
That said, the author has the responsibility to see a specific character's trait to the end. Mary's WHOLE story is that she's fucked up and MC's aunt tells you to help/heal her. In the game there are often times when you can abuse that trust and take advantage of this way. There is a complex aspect in that kind of storytelling, I won't pick it, but I respect it being told. A character born of some purpose needs to fulfill that purpose and until adding the NTR, you WERE fulfilling that purpose.
In my view, you decided that it was no longer important to focus on that purpose. Instead, you wanted fetishes. NTR is one, and you added it with Mary arbitrarily. The girl who's whole angle is healing, all of a sudden has a rape/NTR path? You asked me if having the option bothers me, it does because the conceit of her character, in my opinion, is thrown out. The character built up by your earlier updates amounts to a fetish folder of the most fucked up things you could add. THAT is why it bothered me.
I'm also a writer and have a game. But even if I wasn't, I wouldn't do that. You could have made ANY new character and added a story like that, but you choose to do it with Mary the one person in this VN that could use a break.
Anyway, I don't mean to batter you with my critique. It's your game, you do what you want. I'm just disappointed cause through all the other people complaining about the game and the bugs and systems/sandbox, I really enjoyed it. It sounded pretty wholesome, not so much anymore.
If you wish to talk about it more, send me a private message. I'm sure you can find me