As a footnote, if you're talking about the Herzog film, then your assumption is correct - he worked in that branch of cinema verite that called for casting "real people" moreso than actors.

Aguirre, Wrath of God was filmed 10 years before Fitzcarraldo, but I'm pretty sure using something like the same techniques, and definitely with the same aesthetic approach and in roughly the same location, which is worth bringing up only because the later Amazonian production was chronicled in the documentary Burden of Dreams.

So as far the 1970s and 1980s go, the height differences are as accurate as you could expect from a feature film.

The people Herzog was filming were the Aguarana.