A few experiences to share: We have rented cars four times now in Chile. Twice we have had problems with reservations made in the United States. We had confirmation numbers, but the local offices showed nothing in the Chilean system. This happened with Budget last year in Temuco, and with Hertz this year in Valdivia. In Temuco, there was nothing whatsoever available, so we had to change our touring plans all around. In Valdivia, the Hertz office honored the reservation anyway, but we were lucky that a car was available. These smaller cities' offices don't seem to have a large inventory of vehicles, so that can complicate the problem.
When we rented at the Santiago airport with Alamo, the car was readily available. The price was quoted in US dollars, which we had wanted because we hoped to avoid foreign transaction fees on the credit card. That didn't happen. Not only that, but they used their own exchange rate to compute the price in Chilean pesos. So we got hit twice on that one.
After the Valdivia problems, we thought we would call ahead to Bariloche, Argentina, where we had an Avis reservation. That one was in their local system. Last year, when we left Chile for Mendoza, we also had an Avis at that airport, and that reservation was in their local system.
I don't know if the problem is with the US sites, or the Chilean ones. I don't have any idea why the Argentine system has worked both times, or if that is an Avis thing. I don't believe that anything shady is going on with the reservations, which can be the case at times. Like in St. Martin a year ago. grrr. But be mentally prepared to deal with issues.
Also, car rental prices in South America are generally high, so don't be surprised at the quotes that you will get on-line.