you approach the stopping area in second gear.
when you front tire crosses the que cone you are to stop in the shortest distance you safely can downshifting to first during the stop.
by leaving the clutch in there is one less thing you have to worry about so you can concentrate on the stop and downshift. if you do a compresstion stop(downshift) and still stop within standard for your speed you won't be assessed any points.
i like to tell my students that on the street if you have to do a quick stop you want to be ready to get out of the area incase the car behind you cannot stop in tme or is not paying attention. so make sure you check your mirrors when you stop and always have an escape route planned. downshifting will get your motorcycle ready for a quick escape.
to ignore the facts does not change the facts