Well, spending a day at the ski resort and going back down to a mile above sea level is a bit different than staying there for a long period of time. My brother and I used to go to Mount Whitney often, but he got altitude sickness after camping for a week. I'm no doctor, though, so this is nothing more than simple wondering. Maybe if there were any colonial records of altitude sickness in early Peru or even during conquest, that may help some.
I'm not sure if Patagonia counts as the best in the world, seeing as it's mostly dry plains and cool deserts. Unless it's along the Rio Negro, maybe. But IOTL the Mapuche did wind up establishing themselves across much of northern Patagonia, including the Rio Negro. They had horses by that time, though.
Plant-based agriculture would stick to the few rivers in Patagonia as would most of the population. Some varieties of potato might be able to brave it elsewhere. But just as the steppes were/are excellent for sheep IOTL, so would the Mapuche find good llama pasture there. Of course, they may not know it but there's definitely plenty of fertile land north of Patagonia, which, as far as central Argentina is concerned, is already occupied by agrarian societies; some of which are used to fending off invaders and fortify their towns accordingly.
That region though is also interesting in itself -- many of the peoples in central Argentina just before Spanish arrival were becoming 'Incanized' at that point...or at least obtaining goods and borrowing practices from that region, such as metalworking and llama herding. It would be interesting to see what happens in that area without Europeans.
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