First and third are because most saddle the first two billets are sewn together on the same piece of nylon, or together in some way depending on the maker of the saddle, and the third billet is sewn into the saddle separately. If the first billet breaks or pulls out for some reason, the third billet strap is unaffected, and you can have the time to get off, and it will prevent the girth from falling off completely and swinging underneath the horse. Same with if the third billet breaks, the first one is safe.
As for the trainer, everyone has a little different method for teaching, and if the students are learning properly and advancing, and getting what she's trying to teach them, then I would just ask her next time you see it, why she put the pads the way she did, or why she used the pads that she did, just in the interest of understanding her and her methods better. If you are concerned about her answers, or don't like her answers, then I would let her go, and find someone else.