By that logic, the fatality rate in NYC skyscrapers on 9/11 was something like 1500%, since there were <200 skyscrapers and ~2,700 people died.

It doesn't make any sense. Your numerator and denominator need to use the same units. The rate of fatal accidents was 2/135. The rate of crew fatalities was 14/355. The rate for crew-flight fatalities (separately counting multiple flights by the same person) was 14/852.

If you were evaluating your risk for another flight, the number of crew aboard doesn't affect the risk and it's pretty reasonable to assume that an accident results in either a 0% or 100% fatality rate, so the relevant figure would be the fatal accident rate of 2/135. If your flight follows that profile then that's your probability of dying in an accident.