I would agree with you that assimilation and cultural pluralism have a "profound presence" in the story. I also agree that most of the cultural assimilation takes place before Cal's birth. After all, Cal is three generations removed from his/her immigrant roots. On the other hand, cultural pluralism has a place throughout Cal's life.
Consider the fact that though Cal is growing up in America, attending American school, and for the most part, living as an American, his/her family situation is more of a typical immigrant story. Desdemona and Lefty come to America and move in with family. They work with family. They go to church with family and other Greek immigrants. They fall in love with family and other Greek immigrants. Though in America, Cal's family is very clearly a small group of people who are maintaining their cultural identity by associating so closely with each other and no one else.
Consider also that both Cal's father and grandfather were mostly poor. Though there are times of abundance, they are generally unlucky and/or unwise in their business endeavors and often must rely on their family to bail them out or take care of them. Even Cal's brother, referred to as "Chapter Eleven" (ironic affection), seems to take after his father in matters of responsibility. The love stories of Cal's parents and grandparents is also similar. Both relationships stem from love, loss, and necessity. Additionally, though each successive generation seems to lose a little more of the religious and cultural Greek tradition, its presence is never completely gone. This is likely where most of the family guilt comes from (portrayed most strongly through the female characters).
As both a woman and a man, Cal embodies several qualities of both the maternal and paternal sides shown in his/her heritage. Sure, it was necessary provide the family and historical background of Cal's parents and grandparents in order to show exactly how Cal came to carry the unique genetic defect which causes hermaphroditism. But instead of emphasizing a medical or scientific tone, this backstory succeeds in heightening family heritage, Greek heritage, cultural humor, and religious tradition. It also succeeds in heightening the many facets of Cal's identity confusion.
The strength of these themes in the backstory make it is easy to forget the horrors of war, the incest, the illegal activity, and the social adversity that also weave this family (and Cal) together. By the time Cal is an adult, despite what he has been through, what he still struggles with in the world of relationships and sexuality, and the identity questions he still seems to be grappling with, the sheer strength of the history and culture he naturally holds removes the reaction to see him as a victim.
I don't know about you, but I loved his family and his family's story. Through everything, they are survivors. As members of a young nation, they are also constantly adapting and assimilating to new social and political trends. Because of this, I never felt sorry for Cal, and at the end of the book I somehow knew he was also going to survive.