It is possible that James Owen was mistaken and didn't notice David Faraday and Betty Lou Jensen in the Rambler, but for now we will take his account in good faith, and assume they were not present in the front seats.
It is extremely unlikely David Faraday would have just remained in the pitch black turnout for any considerable time, if another vehicle had pulled up alongside them. So it is likely that the vehicle that James Owen saw alongside the Rambler had just pulled into the turnout before he arrived. Approximately 30 seconds after he had passed the turnout he "thought he heard a shot." Many observers have speculated that the Zodiac Killer had already forced the couple from the Rambler before James Owen arrived. He was about to murder the couple when he saw or heard James Owen's vehicle approaching, so improvised and forced the couple out of sight between the vehicles. But we have a major problem. James Owen does not mention the car doors on either vehicle open, particularly the Rambler. This can be simply explained away, in that the killer, keen to avoid drawing unwanted attention, closed the Rambler door before forcing the couple out of sight.
It has been suggested that James Owen likely didn't see the couple in the vehicle because they were 'making out' with the seats reclined. This would be highly unlikely once a second vehicle had pulled alongside them, in extremely close proximity.
It was a dark, isolated turnout, late at night and anybody would be reasonably apprehensive at this point, and David Faraday, a conscientious young man, accompanying a girl on a first date, would certainly have been aware of the dangers.
If James Owen was correct, and the couple were not in the vehicle, and unlikely they were under duress between the vehicles, then where were they. Raymond Grant has presented his version of events in 'Zodiac Killer Solved', but here we will explore some alternatives. The simplest, is that the couple were in the vehicle, but James Owen simply failed to notice them.
If they were between the vehicles, then we have to believe that the killer pulled up alongside the Rambler, forced them out of the vehicle with warning shots, out of the audible range of James Owen's approaching vehicle, but didn't strike immediately. The assailant then noticed the vehicle of James Owen approaching, hiding the couple out of sight and closing his door, and the door of the Rambler. Once he believed James Owen had passed beyond audible range, he began his attack. Just before he left though, he reopened the Rambler door for no reason. Unless he decided he wanted a souvenir from the vehicle. But with nothing reported missing from the young couple, the murderer either didn't find anything of satisfaction within the Rambler, or this chain of events never occurred.
The final alternative, if we dismiss the above, has been presented by Raymond Grant, in that the couple were held captive, contained within the trunk of a vehicle, likely the Impala.
It is not a valid hypothesis to argue the killer entered the rear of the Rambler, forcing the couple out of sight as James Owen passed, because the rear doors were discovered locked by investigators. Either James Owen was mistaken and he failed to notice the couple in the Rambler, the killer opened the front passenger door after the murders to possibly collect a 'souvenir' or for some ulterior motive, or a third unexplored option exists,
one not dissimilar to that suggested by Raymond Grant. It's a question of whether the simplest answer is the correct one.