Well they were just raiders, and the Incas assimilated all the ethnic tribes in the Andes, and if they fail at that, human sacrifice always works. Besides, the Inca Population lived in the mountains for centuries at this point, which there more adapted to then the Europeans, in fact, they evolved features to deal with the hostilities of the Andes. They evolved larger lungs and larger fingers for plant harvest.
They'd have an advantage of a Conquest of Patagonia.
Not, they don't, most of the habitable zones of chile are at relative low level above sea, 500 meters or so.
The principal problem that the spanish have in his conquest of Chile, is that the andes don't have a plateau south of Antofagasta, and that most of the country south of the Bio Bio river was Cold Jungle, the so called Valdivia Rain Forest.
https://en.m.wikipedia.org/wiki/Valdivian_temperate_rain_forest
Here a photo of the place todas after years of logging and farming