Spoilers, i guess?

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In my opinion, El Topo’s theme works PERFECT as a prelude to the chaos.
It sounds like a cavalry charge, a light brigade slamming against your ranks.
It’s heroic, while at the same time it’s threatening.
It fits with the character of El Topo, because he IS indeed the cavalry brigade, he IS an army, and he IS god.
This is shown when he goes against the general at the start of the film, he’s an unstopable force that ends an entire regiment of bandits holding a town with nothing but a few throwing knives and a revolver.