IMO it seems to me that since you didn't like the story of the game, and now the DLC, you are trying to find ways to poke holes in the whole thing lol. Which is also fine, don't get me wrong haha. To each their own. I still don't see any problems with Daughters and the main game. Eveline doesn't have control over the Bakers. Which is why Jack tries to kill Ethan, when Eveline decides she wants him to be her father. She has no control. She can influence strongly sure, especially those she mutates the most via her mold, but never full control. And Daughters is the very beginning of the infection. Marguerite doesn't notice anything because, the infection, very much like we see with Mia, comes and go. Mia is sometimes human again, and something mutated and invincible. Zoe has the D-series head? Well it IS 3 years later, and from Daughters, we see how she's the only one who immediately remembers Eveline. It's obvious that the infection doesn't affect people in the same way everytime. Who knows what she's been doing for those 3 years. She managed to survive, unmutated and sane. I have no problem with her finding more about the head during that time.
It's also clear that Eveline is different than any others "Series" they've done. She's the first, E-001 and it's obvious that they didn't know the true extent of her powers or how she operates. Which is why her handlers, Mia and Alan were taken aback by how much mold she could actually produce.
In all honesty, I can't judge y'all for playing a game you obviously knew wasn't up your alley. I mean I knew deep down I'd hate FFXV, but I still bought it, platinumed it...and yeah I hate that fucker to pieces. It's nothing like I wanted from Final Fantasy. I knew I'd hate the damn thing the day they announced a party of males only. But...gave it a shot. For other people, it's clear that their FFXV is RE7. It's obvious we'll never agree on RE7's story, like most of the RE fanbase can't agree on any damn game in the franchise. So...meh, let's leave it at that lol. I do 100% understand where you are coming from though.