You know after replaying the opening of part 3 I did get a weird feeling of a reason that might make sense and that could be a bit hard for Steph to tell while loving him, maybe was based on her looks in that scene. If that would be true the game misses an important warning tag, what if she is his half-sister from that father?
Well if that would be true, it will be important that steph will be missable, not everyone likes that tag added later even if I would not mind.
With the information we have so far, pretty much anything is possible. Your new hypothesis in particular would explain a lot of things. And generate a lot of new questions.
But given patreon restrictions on anything incest related, I would not count on that. Given the current production level and setting, I can totally see dev trying to push it on steam later as acting lessons or being a dik. Although, I also know that sisterly lust is on steam, so I have no idea how that story would without incest (pretty sure steam does not allow incest either, or does it?)
I guess for now the best thing we can do is wait to see how it unfolds. I know I am in the minority here, but putting myself in MC place, I am willing to give her a benefit of doubt.
First, because I want to know what she has to say. I can accept she being married and a lot of stuff, I explained it before and got super facepalmed, but I stand by my previous statement (I try not to hold people to higher standard of those I can hold myself against). The disappearing act is what is so hard for me to forgive.
Second, I know, it is late, years passed, she fucked up badly and I could see MC telling her to fuck off and be justified. But if I was in HER position, regardless of what happened, I would like to have the opportunity to explain. If after explaining myself, MC still decided he wanted me out of his life, I would accept it.
Back to your hypothesis, from what I have seen in this forum, most people would not mind. If anything, it seems to be an accepted quirk by most. The other hypothesis, that was mentioned above, that Chris and her may have had something going on between them, now that would be a bitter taste for most. Specially cause Chris is an amazing friend character. He is not the silly horndog, is not the submissive guy just to make MC look better neither is the pedantic douche that you know is gonna go villain at some point. So that would be a way harder hit for most players. I find it really hard for that to be the case, though. Which would only made the surprised hit harder if it is true.
I have a few guesses of why she reacted how she did, but nothing really to sustain them, wishful thinking more than anything. So for now, I wait.