"a man could be the father of his son's flesh,but that did not mean that he was also the spirit of his father" explain the line.

Here, this line has a very simple meaning.

Through this the author simply wants to indicate to the fact that ( a man may be the father of a son's flesh ) a man may give birth to his son....may be responsible for his physical features his looks, but that definitely didnt mean that he was ( also the father of his spirit ) also responsible for his inner soul...In our daily life too we see a lot of such cases somebody may resemble his/her parents in looks but be completely the copy of their uncle or aunts in their day to day behaviour. 

In this case this sense is confined to his UNCLE KHUSROVE nad COUSIN who are definitely not a father and son but completely resemble each other in the way they behave.