Yes rider swaps and fastpasses are both scanned by the same reader.
To answer your second question I will describe two different situations that happened to my family on my trip last February:
1) Using Soarin as an example. My Son had a FP for Soarin between 11am-12pm. We got to Soarin and told the CM that my wife and son both had a FP, but my son needed a RS so he could ride a second time with me because I had to stay back and watch the baby. The CM then scanned his Magic Band. So at that moment, my son now had a FP and a RS for Soarin. Next he scans his band at the FP entrance to Soarin. The system removes his FP but keeps his RS on. He comes off the ride, and goes through the FP entrance a second time. This time the system removes his RS.
2) At Seven Dwarfs Mine Train, my wife had a FP for 2pm-3pm. I had a FP for 11am-12pm. We approached the CM at 11:30am and asked for a RS for my wife. When the CM scanned her band to load the RS, he said he could not load the RS because she had a FP for that ride later that day. Instead he said he could cancel that later FP and give her the RS right now.
So from this I believe the rules are that a person with a FP can only get a RS if he is about to use his FP at that moment. Once both are loaded, the system knows to take the FP first.