Aha, then I understand! In my training, a "clear" drill was always concluded by firing in a safe direction (e.g. the ground), so I would regard that trigger pull as the conclusion of the clearing drill, not as "treating the weapon as unloaded". The point of that step was exactly the mentality that "You just cleared the weapon, so obviously you should treat it as loaded and fire a shot into the ground to re-check that you actually cleared it".