Patagonia is a wild place to travel. Some roads are in really bad conditions. As a matter of fact, we have had 2 rental cars flipped over in the last 8 years!!!
Drop off charges are very expensive. We are talking about USD 1790 if rental starts in Santiago and ends in Punta Arenas. These high drop-off charges have made many persons change their plans. If you want to travel from Santiago and south, I would recommend rent one car in Santiago and returning it to Puerto Montt at an extra drop-off fee of only USD 450. Best car rental deals are when the rental starts and ends in Santiago.
I would like to advise you that Insurance companies (in all Chile car rentals) only cover 100% of driving in Patagonia when a rented vehicle is a pickup truck, jeep, or 4x4 SUV ... not a subcompact or sedans! Therefore they will not cover damages if you do not have a suitable vehicle for the area. In other words, car rental companies won’t ask you where are you headed during your trip and they will rent anything you ask for, but you must know that insurance companies will not cover damages because you got into bad roads without the “proper” vehicle (Argentina Ruta 40 for example). For the area between Santiago and Puerto Montt, any car will do ... but Patagonia is a different story!!!
If you are planning to rent a car to drive in Patagonia, the best alternative is either a pickup truck (because of its higher clearance) or a jeep. Double traction would be better, but simple traction is good enough. We recommend taking 2 spare tires and a spray for emergency flat tires, because distances between cities are quite big, and also because some roads are in very bad conditions. But on the other hand, we have had many clients that have traveled through all of Patagonia with a simple compact sedan (you obviously would have to drive slower and preferably with less weight).
Punta Arenas and Puerto Natales are two locations that allow renters to return their rental car in Argentina. Could be Calafate or Ushuaia.