...the assumption being that the risks are separate. This is clearly false - you are not rolling dice here, the probabilities of the same disaster at geographically "close" cities are linked.
That is, if the probability for each city flooding is 0.002 but the different cities are positively correlated, then the probability of at least one city flooding is lower than it would be if they were uncorrelated. (Because the probability of no cities flooding is higher, because of positive correlation.)