Honestly dude that's wishful thinking on your part. The Dev has had several opportunities to add incest to the story if she wanted to and outside of potential step-siblings in a relationship/having sex, it's either been avoided or outright denied there will not be any of that goin on in this story. If that were the case, it would have been far too easy to have the MC pursue his own mother along with the neighbor after catching them fooling around in the pool. People are always just going to see what they want to see, even if confirmation is there its either unintended or just not happening.
Getting back to the MC's dad, sure there might be a resemblance, but I'd sooner believe it's coincidental at best or maybe an even more logical explanation is the MC's mother had a type of guy she liked in college and happened to be with 2 exotic looking guys who were somewhat similar physically, but with different personalities. If anything, that's just as likely and more realistic than what you've proposed.
My guess: i think that Santiago is Layla and Alexis' stepfather. The principal married him after having her two daughters from a previous marriage, or something. I find it weird that Santiago already was in a relationship with a woman and had a two years old girl when met the MC´s mother, and had impregnated the same woman with a second daughter more or less at the same time he was impregnating MC´s mother...
The dev seems to like mirroring situations. The MC has the same problems when he lived with her father that now that lives with her mother: he has to choose between two sisters. In his old town, the problem was they were going to be actually his stepsisters since his father was going to get married with the sister´s mother. Now could be the same: the problem, when discovered, would be that actually Layla and Alexis are stepsisters of the MC if actually Santiago is the stepfather of the girls and the real father of the MC.
It would be a somehow "dramatic" situation, but without adding real incest to the plot and a making the MC a modern Oedipus that fucks his sisters without knowing it, and probably has a terrible fight with his real father as he has with his stepfather, or something like that... That would be way too much drama for a game like this one, IMO. Greek drama.