This is interesting, but I'd like to see a version where the dots are sized in proportion to the total human population of the time. For example, let's compare just the Spanish Flu and COVID-19.
For Spanish Flu, let's use the low-end number of people killed (50M) and high-end for population (i.e., 1920 numbers -- 1.86B). For COVID-19, we have 27M killed and let's use the low-end for population (i.e., 2019 numbers -- 7.765B). This will tend to under-estimate Spanish Flu deaths and over-estimate COVID-19 deaths (so nobody can accuse me of trying to fudge the numbers to make COVID-19 look less serious).
Using those numbers, Spanish Flu killed about 2.69% of the world's population. COVID-19 killed about 0.35%. So an illustration based on proportion of population would have Spanish Flu's dot 7.68 times bigger than COVID-19's.
Would be really interesting to see how huge the ones further in history like the Black Death and Columbian Exchange would be using that method...and to see how the trend is toward smaller and smaller dots as we become more knowledgeable.

Fascinating story. BTW though, I think you forgot to include the link! ;-)

https://longreads.com/2017/09/05/atomic-city/

"Trick of the Light" by The Who is probably my favorite in the 'songs about prostitutes' genre :-).