But that makes no sense in context of everything that happens in the story. Jon actively acknowledges that everything is happening by chance, and that he can only predict what happens thanks to his ability to see the future. Jon's weakness is that he observes chance occurrences but doesn't act to prevent them (as Comedian helpfully points out after Jon reprimands him for shooting a pregnant woman), because has all this power but is still, ultimately (and not unlike Moore's Joker), a normal man who was very unlucky this one time.

In fact, his profound realisation that there is no God or higher consciousness running everything is what prompts him to escape our own reality and create one in which he IS the higher consciousness.

He acknowledges the Douglas Adams truth that "Anything That Happens, Happens", but that does not at all mean it always was going to happen. Anyone could have been locked in that reactor core, it just happened to be him. Same as the cat in the box (which Moore cleverly references with Bubastis when Ozymandias attempts to kill Dr. Manhattan); just because you observe that the cat is dead doesn't mean it was always dead, or that it was predestined to die in this box, at this time.

Predestination is one of the most pessimistic concepts ever, and Jon ends the story with a very optimistic viewpoint.