Yeah, what you're talking about is caused by the way Deep is pursuing several different routes, that will ultimately have very different outcomes, with the same content. This sometimes results in content that appears to be incompatible with whatever outcome you hope to achieve. So you get loads of scenes with Andrew, even if you've decided to get rid of him, that seem to be aimed at finding some accomodation with him. That's because the middle route, will likely follow some kind of NTR path, because how else will Anna be able to continue her 'cheating' lifestyle longterm, but stay with Andrew? And then of course, the third route will have Anna ultimately abandon this lifestyle and return to being Andrew's loyal girlfriend again. So it's not really surprising that some of the current content feels wrong, because depending on where you want to end up, it definitely is in some instances. And the same goes, for if you want Anna to achieve a submissive or dominant outcome in end, a lot of the content seems to be going in the wrong direction?
Chapter 1, was much more linear. Deep didn't open up Anna to as many possibilities, and therefore it was much easier to reuse the same content for everything. But now that he is opening her up, this seeming incompatibility of some scenes is much more apparent, and understandably perhaps pisses off some people. Reusing content for different routes, even when it appears to contradict earlier choices, is of course a well established method of saving time. It's not ideal, and I'm sure the Devs are well aware of how a lot of players feel negatively towards this, but it's just how they've decided to cut back on development time. And that's the reason for it in the game, pure and simple.
In the longterm, it won't make any difference, Anna will break up with Andrew, if you made that choice, or she'll continue cheating on him and the game will morph into cuckold territory, or she'll get cured and her libido will eventually be reduced to more normal levels, so she can become Andrew's loyal girlfriend once more. And currently the rationales, are that Anna is biding her time if she's decided to leave Andrew, giving him more time to recover from his injury, before she drops the bombshell on him, that she no longer loves him. Or that she's currently manoevring Andrew towards acceptance of her cheating, if she ultimately wants to stay with him, but not get cured. Or that she will get cured, once it becomes available, and will abandon her current lifestyle (which has been forced on her by her illness and circumstances) because deep down she still really loves him and misses what they once had together.
At some point, one assumes, the Devs will separate these paths out. But when that happens, it will clearly mean some updates when you don't get any content, if you're not interested in a particular route. And you can imagine how negatively certain people on this site will respond to that? So at the moment, they're trying to delay that moment for as long as possible, by reusing scenes even if they seem to be incompatible for certain routes. It's the classic problem with much game development, you're damned if you do, and you're damned if you dont.