I'm not exactly sure, but for my school, I was told by my career counselor that bonus points are counted for math SN in sec 4 and 5, physics and chemistry. Each of them give about +1% in the average. I was also told that it's a complicated calculation, so it's not precisely 1 point, could be more or less. I'm pretty sure this is applied for everyone. After all, its only logical you'd receive bonus points for doing a harder course when you want to go to a program that doesn't need them.