Well, in order for me to reverse the two finger scrolling and three finger swiping, I had to install Better Touch Tool and Smart Scroll.
It is very strange. It seems to mess with my head when I toggle the settings back and forth. Like someone said, the default way is like moving the window over a page, while reverse gestures are like moving what's inside the window. I guess I am used to the default way just from using a Powerbook G4 for so long. But reversing it seems natural when in the state of mind that you are scrolling as if you're using an iPhone. I am sure I could get used to it if I used it long enough, but I just find it weird how both feel natural, but trying to figure out why seems to exhaust my brain.