To equate the process of genetic change between parent and child with the theoretical genetic evolutionary change from one species to another is erroneous.
With respect to the latter, the larger process theoretically involves natural selection and speciation. And as you point out, it involves a significant variation in time. So you see it is very different from intra-species change.
So if a 0.001% in DNA is observed in a population over 20 years (all from germline mutations passed on from parent to child), what is going to prevent a 1% DNA change over 20,000 years (all from germline mutations passed on from parent to child)?
If we have two separate populations that change at that rate, what is going to prevent a 2% change from accumulating between the two populations over that amount of time?