If it looks like he doesn't have one now, check out his hairstyle then and now. An afro is going to create a different impression than a crew cut. Take the haircut into account and some of the impression you have of unnaturalness goes away.
In any event, there have been many big-headed kids whose parents told them they'd eventually "grow into" their big heads. Maybe Obama did just that. But it does look like big-headedness ran in his mother's family.
You also have to consider the problems with cross-racial identification. Does Obama really look anything like Malcolm X, or is that just because two black guys in the same pose with similar haircuts look similar to people who aren't black? What looks uncannily similar to same white people may not strike African-Americans in the same way.
Maybe the big black kid in the school picture is always going to look a little out of place surrounded by smaller, whiter kids. Maybe the shadows on darker skin are going to look strange in comparison to the shadows on the other, lighter-skinned kids as a matter of course.
I'm not saying retouching wasn't done in any of these cases. It's entirely possible that the photographer who took the African picture played with the background to attract attention to Obama. But that doesn't mean it's part of a larger conspiracy.
Sometimes he has a microhead.