Well, when you have your hands around the tongs which is holding the mouse and you also have your head hanging over the snakes cage so you can see what you are doing, the snake can get destracted by you moving and by your heat. This may then trigger the snake into thinking your hand is the food, even though there is its real food in front of it. Also, the only time you handle the snake with a feeding box is when you put the snake IN the box. When the snake is finished, you put the box in the cage and open it letting the snake crawl out on it's own, or some people may just have the box/bag in the cage the whole time, then check if it's finished, if it is, just open the box/bag and the snake will crawl out. Another thing is, if the snake is destracted by your hand every single time you feed it, it is going to think that your hand=food. So everytime you stick you hand in or around the cage it's going to think, Oo, feeding time. That is why feeding boxes can be a good way to feed a snake. 1. It's not being destracted by you or your hands. 2. It has it's privacy to eat. 3. You barely come in contact with the snake except when putting it in the box/bag. Like I said b4, this can reduce your risk of being bitten. Also, it may make a snake calmer during feeding because it's alone with not destractions and it doesn't think you're food.
I don't want this to offend anyone, but these are just my beliefs.