I suppose my confusion comes because I'm not really aware of any significant demographic shift in either of those countries in the past couple thousand years, so I wouldn't have thought the distinction of "indigenous" vs "non-indigenous" to be super relevant. I would also typically consider the connotations of "indigenous" to imply some degree of colonization, meaning that unless there's a group of people I'm not aware of, an "indigenous German" is just a "German".
Today you have native Germans and German citizens. Like the same as Brazilian citizens and Native people, i guess? To Imagine the same scenario that we Germans want to enforce in Brazil like "Give the Forest back to the Indigenous People" or "Let them live as their ancestors lived originally" but with people from Thuringia, Bavaria or Saxony claiming land to live how their ancestors lived back in the days is either bizarre or hypocritical.