I'm glad you've liked the game so far
About the call, note that the father is as clueless about what's happening as the MC (and the player). He is guessing what's happening and his guess is as right or wrong as anyone else's. The calls won't change the story. They only give another perspective and give the player, in future calls when he's not guessing, information about events in the past. This information can change the player's perspective, but not the story. Edmund's story arc is optional because it doesn't affect the story. At the start of the game, he is clearly the Bad Guy, only interested in money and his bimbo. His calls will explain why he is interested in them in the first place, and perhaps while continuing to be the bad guy, he's a bad guy (losing the capital letters) for good reasons.
Eileen's backstory is another beast and is optional for another reason. It will resurface as non-optional later in the game in a shorter version. The MC is aware of the situation years ago, and in the first meeting with Eileen, she says her father has resumed drinking, so the shorter version is enough for the MC and for some players. For the people like me, who want to know everything about a LI, it is a hard choice, but the player who chose reading the backstory, rollback, and having sex won't be penalized.
The cloning/spying subplot is unimportant for the MC right now because he is unaware of it. It will be solved (in its first phase) without the MC (player) interaction. The world doesn't revolve around the characters and there are forces unbeknownst to them that have their own agenda and a lot of means to carry that agenda forward. Luckily there is more than one force in place and they are countering each other and the characters go through life dodging bullets they don't even know have been fired.
There are no bad endings in my dorm. For me, the worst ending is the player rejecting all the girls and playing a celibate playthrough, so don't worry about a hidden choice that will lead to a bad ending, a girl dying, or something like that.
About the harem development and how it will become public, my idea is to create mini-harems where two or more girls become aware and accept the existence of the other(s) and then merge the min-harems into the big harem.
Take this example (and I'm not saying this will happen just this way): Scarlett + Daphne right now are on the path of becoming a mini-harem. For them, they already are, but the MC is yet to realize that he's in a relationship with them. Erika knows about Norah (but Norah doesn't about Erika) and accepts her. For the example's sake, let's say Norah becomes aware of Erika and also accepts her. You have two mini-harems that can become public when someone slips in a mother/daughters chat. Once every one of them has accepted another girl, it's easier and less dramatic to learn there are two more girls to share the MC with.
Sorry about the text wall, I hope I solved some of your doubts
