The claim in the documentary is not that that version of the Zapruder film was correct but rather that a provocateur who was trying to influence someone had intentionally doctored the film to manipulate them.
The documentary was not saying this was real, the floating tree was in fact offered as evidence that the film showing the driver turning around and shooting JFK was doctored.
https://np.reddit.com/r/JFKassasination/comments/1b3zb27/the_floating_tree_american_conspiracy_the_octopus/ksxvy6h/