It’s certainly true that genetics is modeling much more complex systems than is typical for physics, and genetics models are correspondingly less precise. Even so, your statement seems a little sweeping. QCD was considered a viable and valuable model for decades before it could be used to calculate something as basic as the mass of the proton to within an order of magnitude, wasn’t it?
You seem to have confused two different sigmas. The sigma you’re talking about is the sample standard deviation, while the relevant sigma is the standard error on the mean, which is sigma/sqrt(N), where N seems to be about 10 million. In HEP terms, it’s analogous to reconstructing 10 million decays of a broad resonance and asking how confident you are that you haven’t gotten the rest mass wrong by a factor of five. In reality, this case is a little different, since we really want to know the maximum true age of four non-coalesced lineages, since that sets a limit on when a two-person bottleneck could have occurred. As I recall, @swamidass used the median of the estimated ages, which seems a conservative choice.