Didn't we see a giant picture of Gabi's husband and everyone said that HAD to be the MC's dad? Which would mean he had sex with his step-mom (technically only; as they had no idea about each other).Scrappy mod is still updated. I think that the link was removed with one of the last update when the mod wasn't updated for more than a week. I have no idea why it hasn't been added back (it might just have been forgotten): https://f95zone.to/threads/intertwined-walkthrough-gallery-mod-v0-10-scrappy.62602/
For me there is absolutely no chance that the MC father is one of the LI father. The author doesn’t add incest in the game so adding unintentional incest seems a no go. If the sisters father is MC father, it would also mean the MC is the result of him having cheated as he was already a father in a stable relation (as Alexis is older and Layla about the same age). However, what I think is a possibility is that the MC biological father is the stepfather of Alexis and Layla (with even the possibility of one or both to believe that he is their biological father). This is something that I would expect more from the author..
There are two men we aren't meeting, that Nyx is dragging out the revelation as to who they are, Layla and Lexi's dad & Gabi's husband. The guy that the MC talks to at the bar, when eating steak, seems most likely to be the dad of L&L and husband to Adriana. Emily knew or knew of him when she was Ana's roommate, I don't see her then having a child with him and Ana staying with him AND both of them not freaking the shit out that their children are dating. Nor do I see Ana shrugging it off and staying friendly with Emily - saying that they have to arrange to meet for coffee, going to her restaurant, etc (I know that Andres was "supposedly" the father but I don't see how Ana wouldn't have been in the know or have figured it out).
My guess is that the two men are friends or, more accurately, former friends. That Emily met Santi through Ana and her husband... Perhaps they were also college roommates and people constantly mistook them for each other.
Honestly, I wouldn't be surprised if someone creates a patch that changes it from roommates to brothers. Which would make L&L and the MC cousins. Marriage between cousins, first cousins even, is more acceptable in terms of 'cest.
All of this is pre-morning coffee so take it with a massive block of salt.