It's an interesting finding. I think I remember discussing it with a creationist on the forum a few months ago who thought he saw support for his superstitions. It was probably Perry. There is a lot of scope for misunderstanding this paper.
It doesn't call into question the fact that extant species diverged from common ancestors over millions of years. It does appear to show that there has been a genetic 'sweep' within the past 100,000 - 200,000 years.
Extant species can be thought of as being like the tips of branches on a bush. They all budded within a relatively short time but their origins go very deep.