The parallels to the European genocide of Native Americans has significant consequences to two groups of people. The first is the white supremacists/edgelords who think an invasion from thousands of years ago means the actions of colonial Europeans as well as ongoing social justice issues with native Americans/reservations are somehow justified or deserved. The second is the far larger but far less dangerous group of people who think native Americans are somehow inherently morally superior and/or that European colonialism is responsible for all the world's problems. To them it's an article of faith that aboriginal peoples do not and cannot commit large-scale atrocities.
These two groups can make discussing and teaching American pre-history very difficult.