I agree, he is the boys father. Believe it or not, this type of think was a common occurance among quakers who owened slaves, I had a great Aunt haliwah saponi/white/african from the south whose daughter married a man whose grandfather was his grandmothers owner, he had eleven children by her, and he owned half the city where they lived, when he died he left his whole estate to her, she became a wealthy women and also her eleven children were related to another wealthy family in another state whose slave owner also took up with a slave women and had children by her, and he left her his whole estate. The families intermarried.
I stayed in contact with a white cousin of mine and we researched wills and found that this happened a lot.