I've seen most of these and admired them (as well as some works of the directors you mention in the conclusion).

I think the greatest controversial film (thought the controversy was a bit staged by the institution depicted in the documentary) is "Titicut Follies."

My favorite film that might be called controversial / contentious because so few people appreciate / understand its minimalist brilliance it is "Window Licker."

The one film I wish more people would see (though it's not particularly controversial per se, so I'm promoting it here anyway) is the 2013 Mexican film "Cumbres" by Gabriel Nuncio. It's a sister road trip, a bit reminiscent of "Thelma and Louise" without the exaggerated Hollywood plot points. Here's the trailer, which might give you a sense of the movie, but it may be difficult to find the film itself (no longer on Amazon Prime): https://youtu.be/AAI0-XQuENE