i honestly do not know what the rubber tip is for... if the pins have been in there for a while, the rubber usually sticks inside the caliper bracket when you pull the pins.

I would guess that at one time there was brake work done on the car and one pin needed to be replaced, so they just got the pin without the rubber tip. Either pin fits top or bottom just fine, but if you want to get technical, the rubber tipped one goes on top.