Upon arrival in Honolulu, customs and immigration authorities would have treated him as an unaccompanied minor with an Indonesian passport. He would have been placed in custody of the Dunhams, supervised by Catholic Charities which was one of the agencies used then and now for such purposes.
Once school started, he was a foreign student and that is why as an adult he needed to be naturalized in a court proceedings. Hence the Brennan led breakin at the Passport office to access his passport and files which are the tell.
Interesting theories