> Ata’s bones contain DNA that not only shows she was human
The fact that there's a DNA already means it's not an alien, doesn't it? Having a life form with the same uber-complex chain of nucleotides as the life on earth developed is as improbable as a server on an alien mothership being compatible with a Macbook. (Quick primer on the subject: https://www.airspacemag.com/daily-planet/cracking-aliens-gen...)
Having said that, the NYT article reads like the researchers are still unable to explain the discrepancies between the age and the well-formed skeleton as well as the number of mutations. Were there any secret nuclear tests conducted half a century ago in Chile? But that would also probably be insufficient to cause all that. I would bet on experiments trying to cause deliberate mutations.