At the time of negotiation and congressional consideration of NAGPRA, no scientific organization, no federal agency, no Native American, no museum and no one on Capitol Hill was confused by the definition of "Native American." Everyone understood that NAGPRA applied to human remains and sacred objects pre-dating the United States.
The court ruling created a legal fiction that perpetuated a deception that studies had not already been conducted on the Ancient One. Kennewick scientists actually are advancing a white supremacist theory. In obscure pseudo-scientific legalese, they whisper to reporters and others that they are on a mission to find out if Kennewick Man is a white man and to prove that Europeans were here before Native peoples. They leave out the part that they studied the Ancient One before going to court and already concluded that he was Native and not European.