The question is why did he say this, did he feel the presence of 'Phoenix' psyche of Jean Grey?
Yes, this is why. The reason behind this is because of Apocalypse's entire point of view in life. Survival of the Fittest. That the weak should die while the strong live on. And if that requires the strong to kill the weak, so be it.
The Phoenix is one of the strongest known force in the Marvel universe. While the movie version has been reduced to just being part of Jean's psyche, in the comics, the Phoenix Force is the combined strength of all psionic or life in the universe. Even in the movies, the Phoenix, or it's evil (more like only concerned with it's own self) counterpart, the Dark Phoenix, was restrained by Jean's own morals and old timeline's Xavier's mental blocks.
So Apocalypse's line of "All is Revealed" is a statement that the strongest, i.e. the Phoenix, has defeated the weak, himself. That the strongest is no longer holding back, that the strongest has been forced to attack at full strength. He has admitted defeat in the face of a stronger adversary. It's his goal in life.
More importantly, as he considers all mutant kind his children, he also sees this as the child surpassing the parent.
There is an alternative interpretation. Apocalypse foresees the Earth burning, to force the Survival of the Fittest. When the Phoenix comes forth, he sees that the Earth will burn, by her hands, not his. But that he brings this to happen:
It's the most important line in the movie. But what does it mean?
Let me take you back to the film's beginning. Awakening from her vision, Jean talks to James McAvoy's Charles Xavier about her fears. She feels as though her powers are like a separate entity within her, one that she's afraid to awaken. Xavier dismisses this with far too much ease; and, at the end of the film, he encourages Jean to tap into the fullness of her power and defeat En Sabah Nur. She does so, and manifests a fiery effect that's easily recognizable as the Phoenix halo. In triumphing against En Sabah Nur, she reveals the power within herself. In a telling sequence, her manifestation begins with a door opening and the figure of Jean stepping out of the shadows and into the light. The first trailer even deliberately interwove that scene with Jean's vision!
Now think about that vision of missiles launching (which happened), and ultimately of fire burning across the world. In that moment, En Sabah Nur realizes that all is revealed; he was never the fulfillment of the vision.
The fire that burned across the world? That was Phoenix fire.