Flooding and hurricanes tend to go hand in hand on this part of the Atlantic coast at least, so I can’t say as I agree with your assessment that anyone was discounting that likelihood. Slow moving storms are worse, but some extent of flooding is associated with them all.
There was surprise surge today in Jacksonville. I posted a map upthread about how the tropical storm-force winds massively expanded at landfall. The track of the storm pulled those into Jacksonville and points north, and the long fetch of those winds meant high surge, and that ran into the runoff coming downriver from 15 inches of rain. Sometimes the overall physical dynamics partially dictate the ground truth, and it has nothing to do with what category the storm happens to be at the time.