Please point to these rights and legal theories. Do you just mean NAGPRA?
As far as I know, whatever legal rights any native American people have in the Americas at this point in time are based purely on them being here when Europeans arrived near the start of the 16th century.
Whether they had been the occupants for 400 years or 40,000 years wouldn't make any difference to the treaties that were signed (and generally abrogated).