You are probably right about other states where the White-Negro color line was well established, but it could be that the registrar in Honolulu hadn't seen that many African-American children.
And remember, this was all before the federal government's racial classifications came in. In Hawaii, Chinese, Japanese, Native Hawaiians, Filipinos, and possibly even Portuguese all considered themselves separate groups. So you'd want to go back and look at different birth certificates issued at the time to see how they handled this.
Think back to 1961. If you heard that your new neighbor was an "African" you might have reacted differently than you would have if you were told that he was a Negro or black or colored, so I think it was probably natural that the family would want Barack Sr. categorized in such a way.
In 1961 an African neighbor in a white neighborhood would not have been tolerated and he would have been called nigger, regardless of his nationality, here in the south. That is the way things stood in 1961.