First of all, the same effects can be achieved using CSS, so this is not a JavaScript vs. CSS-based responsive design situation.
The decision to slow down the transitions is purely a design decision - there are no technical limitations on doing it instantly.
In my opinion (and experience), slow transitions are more annoying than aesthetically pleasing, especially on a "utility" website. Also, a screen resize event is relatively rare - most users do not resize a screen during their visit. When users do resize it (for example, by turning a tablet), they expect an instantaneous adjustment. I see no reason not to meet their expectations.