How can flood water come in through a toilet?
The trap on a toilet (or any plumbing fixture) prevents sewer gas from escaping. It's a very low-pressure thing, consisting solely of a small amount of standing water filling a low spot in the drain. Any force capable of moving a little water can overcome it, including air vacuum if it's not properly vented. 

In the case of this flooding phenomenon, there must be a break in the city sewer line somewhere, and water standing above it. This obviously creates pressure that will escape at any point below its surface level.