I just thought of this in my previous post, too: what if he was legally adopted by Soetoro in Indonesia (this automatic under age 5 thing included), but they never even told the USA about this adoption? Maybe he came back here as whatever kind of "US citizen" he was as a toddler, and never mentioned in this country that he was a citizen of Indonesia with a different name entirely.
It is something I've considered. The Passport document listing his name as Soebarko but then having it crossed out tends to make me think something of the sort might have happened. But on the other hand, I would think she would have obscured it completely if she was really trying to hide the fact, and she had accidentally let it slip.