As I understand it, the 3 second interval is the interval of measurement used, and doesn't imply anything about the duration of the expected wind.
If the wind was sustained at 90 mph, then I suppose due to natural variations in the turbulent flow, you would actually have 3-second gusts that were higher than 90 mph, so it wouldn't be a 3-sec-90 mph wind anymore. And if you had a 90 mph-3 sec wind condition, you might find higher speed gusts that had shorter durations than 3 seconds.