This is basically an updated version of Joseph Conrad's book "Heart of Darkness" with a lot Francis Ford Coppola thrown in. The location is Viet Nam, instead of Africa, and as with any update; they thought it would be more relevant than trying to explain the Congo. Toss in some songs from the 60's era ("The Best of the Doors"- `The End'), and some classics (Wagner - "Die Walkure: Ride of the Valkyries"), and you have a movie. Too bad it is not that easy.
I would not worry too much whether this looks like Vietnam or if certain events really take place, as that is not the point of the picture or the intent of the story telling. The feel of the book was conveyed. And I would not worry if it does not match the book story word for word as this is a different media. If you come away with the question "what would I do if it were me?" it worked.
Not to distract from the movie review, however I was in Viet Nam (1967-1968) in an armed reconnaissance organization. And the Vietnam I was in did not have the surrealistic scenes. We did get to see Bob Hope and Martha Ray "The Big Broadcast of 1938" (1938). Before that I always thought it was a bunch of hype. However it did make a difference having them take the time to go there. So I could see something as weird as the bunny scene happening.
Besides the movie there are the Scenes of the destruction of the Kurtz compound set. They were required to clean up after the movie was made. Coppola says that these scenes were removed from the end of the movie so people did not think that it was part of the story. However I saw this on TV and they left the scenes in and I did think it was part of the story.
Another movie interpretation of, "Heart of Darkness" was made later. Not quite as moving as Apocalypse Now, but you should see it to compare to the original, "Cannibal Women in the Avocado Jungle of Death "(1988). Adrienne Barbeau is Dr. Kurtz.