You can safely shift gears according to the speed of the vehicle. If you are moving off from a slope, makes no sense to move off from 1st gear. Instead, shift directly to 2nd. Similarly, when you are cruising at 80km/h and there is a sudden build up from traffic ahead, causing you to brake, you can downshift from 5th to 3rd or 2nd. 

I have a fiat fiorino semi auto van diesel ... I switch to second gear straight after I feel the vehicle has like reasonably "warmed" up but have not done 1st to 3rd straight , the 1st to second gear shift like ' no event ' ; so I go to second straightaway ..... used to do it in previous manual rides