Adam, of the book of Genesis, is believed not to have possessed a navel because he was not created in the physical way that requires the use of an umbilical connection between mother and child. It stands to reason that Eve would not have a belly button either, for the same reason. These two are, in Christian theology, the originals: the couple from which everyone else on the earth comes.
Pilate's lack of naval, to me, signals that she is another such original person. She did, after all, crawl out of the birth canal unaided, after her mother died in childbirth (and she was believed to be dead as well), and her father was murdered when she was very young. There was a great deal of pain that preceded Pilate's life, or occurred during its earliest stages, and yet Pilate seems to have found a life, and a way of living, with which she is happy.
She does things in a new way—traveling around, doing pretty much what she wants when she wants including how and when she chose to love, to eat, to have children, and so on—and, more than any of these details, Pilate loves in a way that no one else around her seems to do. The example that she sets, of how to love so completely, seems to be what sets Milkman on his better path toward identity and self-expression, and though she is not his mother, he learns far more from her than he does his own mother.