The wars we fight today between communism and capitalism mirror the wars fought throughout history between the middle-class and the elites, between Protestants and Catholics, between the early Christians and Rome, etc, back through time. Dick had been trying to see the true world and when he finally uncovered it what he found was that narrative archetype which he had correctly depicted in Flow My Tears. Valis is always on the side of freedom, and the only way for enslaved people to be victorious is by overthrowing the Empire, not merely escaping it.
The AI voice who addressed him is YHWH who he realizes is Valis. Dick recognizes he has declared “he has figured it out” too many times and is hesitant to say that again (since it seems to doom him to uncovering more questions), but he does feel that Valis = God / Christ and that he saw and experienced him in 3-74.