He considers his mother's status as irrelevant to who he is. He is basically saying that he only regards his African Ancestry as defining him, and he is in no part an American.
Of course this is just an offhand comment, so I wouldn't put to much stock in it. I think he tries to tailor his message to the audience, and while he's aware of his mother's American contribution to his existence, he saw no benefit it mentioning it.
This is true, except why identify himself as African and not African-American?? Obviously he’s not a traditional African-American because neither of his parents where African-American, but there’s no reason to say his daughters are descendants of Africans AND African-Americans. In a weird way he’s distinguishing himself from his own wife, except as has been mentioned Obama’s African roots have little or nothing to do with slavery.