@nfzeta
you're being blinded by your bias for him.
I could just as easily claim that you are "biased" for the daughter by virtue of your defending her and overlooking her behavioral flaws. Your earlier appeal to hormones might be a good example of this. However, I can not see into your head, nor you into mine. Let's leave such airy accusations out of this.
No, there is no way that he shouldn't have known as the father.
If the father works long days, his daughter does not speak to him, and the school has not yet notified him, how would he know? He can't keep tabs on her, and she would not tell him or give him signs that she was truant if she didn't want to be found out, doubly so if she rarely speaks to him at all. If he has an inherent trust for his daughter, he wouldn't assume she was hiding something from him. He wouldn't know until the school contacted him about it, which is exactly what happened. Hypothetically, there are ways he could have found out, but if his daughter literally puts a wall between them his options are limited in a pragmatic sense.
You're even assuming that he never sees her and that she never leaves her room.
On the contrary, I'm not assuming anything. We, as readers, have not observed any face to face interaction between the two in either of the chapters. If such a thing happened, it would be shown as a clearly important moment in establishing the relationship between them. The fact that it deliberately has not been shown conveys to the readers that the two never (or very rarely) speak face to face.
While we're speaking of assumptions though, you have assumed from the very beginning that the father was responsible for creating the distance in the first place. You claimed that he "pretty much ignored" her after the mother died, thus implying that she isolated herself from him as a result of his neglect, even though there is no evidence for this in the two chapters we have. Is it not perfectly possible that the daughter isolated herself first, and that the father gradually lost hope for reaching her and thus slackened his efforts, leading to the present situation?
Those are regular Japanese sayings/greetings that one could say even if the lived alone, they're not meant directly for the daughter.
Then how about his apologizing for being at work late, asking if she's had dinner yet, advising her to eat if she feels sick, only to be met with the words "Don't act so familiar with me!" from his own daughter? All of this happens in the first chapter. Judging from his expression after hearing those words, they clearly hurt him deeply, as could only be done by words from a person he cared very much for.
Its even shown in the end pages of this chapter where he goes to her room and says her friends and teachers are worried about her. I don't think he even realises how callous that probably sounds to her, the fact he didn't include himself there. All that sounds like is "You're making me look bad".
To me, it sounds more like "I know you no longer care whether I'm worried, but what about the others in your life?" It doesn't bespeak selfishness but lack of confidence in himself and the aforementioned loss of hope. The father does not strike me as callous, but as exceptionally worried and perhaps somewhat cowed by his daughter's past rejections (based on his being ignored seeming routine, it's been going on for a while). I think how the story will play out is through the girl he is speaking with giving him the courage he needs to reach his daughter in spite of her open hostility towards him.
Perhaps you will say something like, 'there is no reason why a girl should need to give him courage in the first place, if he is a worthy father he should have had the courage already!' and you would be correct. How nice it would be, if everybody had the courage to say what needed to be said, and the ability to mend all relationships! I don't think this is the story of such a father, though. If it were about a perfect father, there would be no story, just so if it were about a perfect daughter. As I said before, both characters are sympathetic and I don't think either of them are bad. Only, the father is slightly more deserving of sympathy on account of the efforts he puts in. Above all, the father realizes his own flaws and wants to correct them (check the scene after the meeting at the school). Neither the daughter nor the father are worthy of scorn, even if words like "selfish" or "cowardly" may apply in spades to them both.