Let me put it another way. If you are flying the LIM/UIO/BOG route without doing an overnight with two flight coupons, in reality you are taking one flight that makes a stop in UIO. This would be similar if I were to fly American from SEA to MIA with a stop in DFW. When I check in at SEA, I get one boarding Pass to MIA. I can choose to get off the plane in DFW to stretch my legs but would use the same boarding pass to get on the flight to MIA. The miles that would get posted to my account would be from SEA to MIA straight!! If I were on a routing that changed planes (and flight numbers), I would get two boarding passes and the miles posted would be SEA to DFW and DFW to MIA. If I asked American to give me two boarding passes for a direct flight that made a stop (but no change in flight numbers or planes), they would not do it. Even if I have tickets issued with two different flight segments, American would still give me one boarding pass.