Main Theme: Japan's preference to choose silence before shame, (and also wincest)
You can see Japan's traditional way of dealing with these scandalous family issues, MC's father got his hands on a minor and his official wife only says: "he was that sort of man" and brushes it off, hiding the truth to avoid shame instead of seeking justice, he got his adoptive daughter pregnant and still gets to walk on and off of their lives without consequences, returns whenever he wants to her daughter (now mistress), later on he ditches her as soon as he finds a younger one and repeats until his body alows it.
The least they could do would be refusing him to return to the family's house/business, still returns and gets treated like the absolute king, MC grows admiring the father for being a "free spirit" and then from childhood normalizes adultery by constantly seeing her adoptive mother and father doing it with other people, unable to separate maternal love from first love, he decides to ran away but maintains the same set of values, almost as a rivalry with his father for taking his Mother (he didn't know) away.
MC's father lived his life without accountability (died from health issues due old age, author tends to draw the characters as young looking despite some being almost 60) and the same daughter/lover he discarded ran back to him and stayed by his side until the last breath, he manages to get her pregnant again before croaking (this part is still inconclusive, not sure if the new girl is MC or MC's father's daughter).
Wholesome indeed