While the film devotes much attention to the contention that Arthur Leigh Allen was the prime suspect for being the Zodiac Killer, in each of his appearances (whether vocal, physical, or both), the Zodiac Killer is portrayed by different actors. This subtly allows for the possibility that the Zodiac may not have been Allen after all, while still treating Allen as the most plausible suspect.
Taking it even further, the picture of the second man Mageau points to - whether intentionally or not - happens to bear a striking resemblance to the real life Rick Marshall, the other suspect discussed in the film.
The film's subtle use of cinematography to portray the killings and place the viewer in the position of the witnesses. The first killings aren't depicted since there were no survivors, while the second and third are portrayed from the victims' point of view. The final killing starts with a birds-eye view of Paul Lee Stine's cab (it's known that Stine picked up the killer at Mason and Geary but since no one was there to witness it the pickup is shown from an impartial viewpoint) while the taxi parking and shooting are shown through a high angle long shot - the perspective of the only witnesses to the Paul Stine shooting, a couple of teenagers watching from the second story of a house across the street.
"Crystal Blue Persuasion" plays during the Aqua Velva scene. Robert drinks crystal blue Aqua Velvas and persuades Paul Avery to try them.
. This subtly allows for the possibility that the Zodiac may not have been Allen after all, while still treating Allen as the most plausible suspect.