I've toured in SE Asia as well as Chile, however none of these tours were longer than a month, not a multi-year affair that you're planning. I was riding a mountain bike with 26" wheels in northern Patagonia in both Chile & Argentina. I rode on both paved and unpaved roads there. I was not on the Carretera Austral, however. The paved roads in both countries were pretty good. Most of the unpaved roads were OK, too, though I recall one or two roads which made me happy I had brought my mountain bike. I would expect that the Carretera Austral would have harsher conditions. You might want to search or post on the PanAm Riders Google group:

https://groups.google.com/forum/#!forum/panam-riders

I have found that the roads in developing countries are often surprisingly good. Two countries I toured in that had pretty bad paved roads were Costa Rica and Sri Lanka, though the road quality in Sri Lanka was extremely variable; some great, some awful.

In SE Asia, I rode my Bike Friday with 20" wheels in Laos & Thailand. Most of the roads were excellent in both countries. I rode a touring bike with 700c wheels in Malaysia & Singapore before I got my Bike Friday, and the roads were good there.