You definitely missed my point there, I didn't care if mia ended up in something like that myself other than the taboo nature and absurdity of the erotic content. Which is why I never understood some of the backlash in regards to the NTR when it wasn't really NTR. The backlash on that ruined any chance of pushing the taboo further. So, I blame the ones who whine about it more than anything, they shot themselves in the foot and now they don't get to have their harem of all the women with the MC (downside for everyone else? Now everything has been tossed out basically. Upside? New direction that you hopefully do a good job with). Myself though? I just don't see this working out as well as you think it will but I am going to give benefit of the doubt since it has held my interest due to the taboo nature of the game for as long as it did. I just hope the taboo nature of the game isn't sacrificed entirely for the nuance you want to try and create. Main issue as best I can put it that hopefully you'll understand is a big pitfall in writing, suspension of disbelief. You turned the story down a route that will definitely need further exploration as to why it happened. Why did emma suddenly become the manipulative bitch? Why did the dad call grace to talk about his wife and suddenly she's making an offer to mia to live with and work for her? What was that about? Wouldn't she call her sister instead and ask what's going on? There's plenty of questions and hopefully you work it out cause the characters are worth expanding on with content. Just don't forget it started off as taboo and that isn't something to just toss out entirely without risk.
I don't see why any of these questions you have need further explaining? Why did Emma become a manipulative bitch? Well, it shouldn't be hard to believe because she certainly was no saint before. She was always sort of cunty. And I thought out of the limited characters I had to work with, Emma would most believably play the role of an antagonist which I thought the game was in need of. Because without conflict, there's no story. At least not an interesting one. And by making her the "bad guy", it removed the need for the MC to be the villain. Which even though he was the protagonist, he always still was. Now, he was on the other side, getting a taste of his own medicine. He was the one getting blackmailed and forced into doing things he didn't want. For once it allowed for him to become a sympathetic character (at least to some extent).
On to your other questions, why did the dad call Grace? Because after their blow up, he thought he'd ask his wife's sister if there was something going on with her, that she wouldn't tell him about. Why did Grace call Mia and not the mom? Because it was established that the two sisters didn't get along, and she was just concerned about the wellbeing of her wayward niece, maybe? And then she offered Mia a job because she sensed how directionless her life was. Makes sense, doesn't it?
I could probably come up with an answer for all your other questions, too. But to be honest, at the end of the day they're all plot contrivances used to get the story to where I wanted it to be in the end. That's literally how every story is. Ever watched cinema sins? Some of the best, most highly paid writers in Hollywood, employ the same tactics to make their story conveniently play out the way they wanted it to.
As for your final concern that the game will somehow lose its taboo nature, I mean, the game ultimately revolves around the romantic relationship between a brother and sister? So of course the taboo aspect will always remain front and center.