Here's the ordering if I delay both articles until later:
1. For the Realm! - intro to Admiral Windsor aka Joseph's grandmother in 3994 AD
2. Boys With a Destiny - intro to Joseph, Apollo, and God, fast forward thru childhood to 4017 AD
3. The Shadow of Death - Joseph's first full chapter, his world and its history, action begins
4. A Pax Romana - Apollo's first full chapter, intro to the shogun, Apollo's destiny revealed
5. Galactipedia: The Great Collapse of Civilization - first major galactic event of the future
6. I Will Shake the Universe - Andrew's hanging, Joseph's destiny revealed
7. Galactipedia: The Rise of the Julii - second major future event
8. Title TBD - intro to the imperator and imperatrix, their relationships with Apollo, the Throne Room
It just doesn't work. Joseph writes his essay before the reader knows anything substantive about the Great Collapse. Also, we then seesaw back and forth between story chapter and Galactipedia starting from chapter four. One of the advantages of having the Great Collapse before the main story chapters is that it gives history that affects both MCs. The New Bethlehem essay is relevant to Joseph. And the Rise of the Julii is relevant to Apollo.
Here's what it looks like if I move the essay out as a Galactipedia article:
1. For the Realm! - intro to Admiral Windsor aka Joseph's grandmother in 3994 AD
2. Boys With a Destiny - intro to Joseph, Apollo, and God, fast forward thru childhood to 4017 AD
3. Galactipedia: The Great Collapse of Civilization
4. The Shadow of Death - Joseph's first full chapter, action begins
5. A Pax Romana - Apollo's first full chapter, intro to the shogun, Apollo's destiny revealed
6. Galactipedia: New Bethlehem
7. I Will Shake the Universe - Andrew's hanging, Joseph's destiny revealed
8. Galactipedia: The Rise of the Julii
9. Title TBD - intro to the imperator and imperatrix, their relationships with Apollo, the Throne Room
This one at least is balanced. Two opening chapters, an article before starting the main story, two story chapters (one per MC), followed by one article+chapter for each MC.