I don't know where you got those figures. As for deaths by the flu, the CDC says that last year (2019), there were 34,200 deaths in the US due to flu. The CDC count of COVID-19 deaths just through October 16 was 204,613. That's substantially higher and doesn't even cover a full year. Remember that COVID only really started to hit the US in March, and of course we still have over two months left to go in the year. Based on these figures, the death rate to COVID is about six times higher than the flu and thus not, as you say, "about the same rate".
It's also higher worldwide.Johns Hopkins Medicine says the following:
COVID-19: There have been approximately 1,099,380 deaths reported worldwide. In the U.S, 217,717, people have died of COVID-19 between January 2020 and October 16, 2020.*
Flu: The World Health Organization estimates that 290,000 to 650,000 people die of flu-related causes every year worldwide.
The COVID-19 situation is changing rapidly. Since this disease is caused by a new virus, the vast majority of people do not yet have immunity to it, and a vaccine may be many months away. Doctors and scientists are working to estimate the mortality rate of COVID-19, but at present, it is thought to be substantially higher (possibly 10 times or more) than that of most strains of the flu.
*This information comes from the Coronavirus COVID-19 Global Cases map developed by the Johns Hopkins Center for Systems Science and Engineering.
(Bolding added.) So it appears from the above that the facts show that the death rate of COVID is substantially higher and that much of the medical community believes that to be the case.
In any event, the answer to the OP's question about the store's rights and obligations when dealing with someone who comes into the store to shop and claims they cannot wear a mask due to a medical condition has already been provided, and this debate over just how bad COVID is doesn't change that.