The Herzog comparisons strike me as facile to the point of blindness as Guerra has none of the thematic concerns of him and the jungle seems to mean something much more benign. While the aesthetic is totally different Pasolini strikes me as a more informative comparison. The compass scene, for example, could never happen in this fashion in Aguirre. Not just for how Theo moves on, but also because the point of contention is moving from one mode of living to another and viewing that as learning rather than necessarily progress in its complimentary usage. Though where the film truly differs from Pasolini is how non-judgemental Guerra frames things. Even he isn't unable to totally present primitive living in a romantic fashion or modernity in harshness, but with having cohabitation there comes a sense of egalitarian choice which Pasolini's strict dichotomy does not even consider. There is a horrible price to pay for knowledge, whether the knowledge of the medicine of the primitive or the business knowledge of the modern, but the choice should be yours. That's why someone like the priest can come across as such a villain regardless of intention or quality. He forces knowledge and keeps things separate like Pasolini (I suppose Pasolini and the guide come across as more pleasant because their sympathies seem less harsh but are probably just as) rather than allowing for choice and combination. What makes spanish less pagan than the other languages after all?
This easily makes the westernized partner of Theo the most compelling character of the film as he is actively dealing with hardships of this transitional period. This is also why the need for two time periods seems so important. It highlights all of the potential avenues that this transition from one set of histories to a mostly unrelated and unified history could have gone down. Perhaps some are better than the fate Columbia now faces, but certainly many are worse (though I imagine the worst of these is shown at such a length in part because it is so cinematic). Knowledge is like a orchard full of fruits which are foreign and can cause a longer life, a shorter life, or just basic sustenance. It is always important to be cautious of which type you are eating though too much caution will cause starvation.
Dealing with this intrusion of potentially valuable information actually reminds me much more of African cinema and literature than anything out of Latin America which tends to have a more Pasolini approach to the past ignoring the sublimation of the mestizo. In post colonial African art (particularly in the western states) there's a genuine effort to not be Gaul or Arab, but at the same time not to lose the benefits they have provided. It's usually phrased as tradition versus the west (which is ironic given how Greece and Italy are east of these peoples), but Guerra handles things much simpler and to my mind better by having it be one set of knowledge against another with history folding them into one whether the people like it or not. Perhaps in a trivial example Guerra reminds me of all sorts of incidents of knowledge becoming history and thus informed thanks to time. Looking just at film the hold out against sound and widescreen seems straightforward now, but at the time was a very serious philosophical debate. Guerra is examining the same problem with the identity of a whole continent and then some.
The film also deals with all of this in some simple moments of intense beauty. When Haydn first plays and time fold in on itself the simplicity of the whole is so strong that it is not hard to cry. The film has found for 15 seconds or so the perfect summary of all of its ideas, yet it needs all that has come before to be truly understood.