My point is that we can't shut up and calculate with probabilities of 0.0001% because we can't reliably measure or reason with probabilities that small in day-to-day life (absent certain very carefully measured scientific and engineering problems with extremely high precision; e.g. certain cross-sections in particle physics).

I know I assign very low probability to Baduhenna, but what probability do I assign? 0.0001% 0.000001% less? I can't tell you. There is a point at which we just say the probability is so close to zero as to be indistinguishable.

When you're dealing with probabilities of specific events, be they XRisks or individual accidents, that have such low probability, the sensible course of action is to take general measures that improve your fitness against multiple risks, likely and unlikely. Otherwise the amount you invest in the highly salient 0.0001% chance events will take too much time away from the 10% events, and you'll have decreased your fitness.

For example, you can imagine a very unlikely 0.0001% event in which a particular microbe mutates in a specific way and causes a pandemic. You could invest a lot of money in preventing that one microbe from becoming problematic. Or you could invest the same money in improving the the science of medicine, the emergency response system, and general healthcare available to the population. The latter will help against all microbes and a lot more risks.