This Belly Button issue sounds like the Chicken and Egg quandry.
My opinion: If God created people, then God made them look just like other people.
Since everyone has a Belly Button, God created the first 2 people to look just like He created the Billions of people who were created after that ... WITH a Belly Button.
NOT having an umbilical cord doesn't mean that a person CAN'T have a Belly Button.
This is just one of the limitations of human minds: that everything must be just like we think it should be.
Garbage in ... Garbage out.