From the interviews I can find, it's appears that Amos' fate was planned by the end of Caliban's War.
This article talks about them planning options for the series based on what the publisher might agree to once the second novel was released (different lengths of the series), but notes that the same end scene was planned regardless of how long it took to get there.
On June 26, 2012, Caliban’s War hit bookstore shelves accompanied by
more positive reviews, helped along by Corey’s able publicist at
Orbit, Ellen Wright. From that point, Abraham and Franck began to plan
ahead. The books were selling well, and Orbit was standing behind the
series. They sat down and drew up pair of outlines, one with nine
books, the other with twelve, each ending up in the same place. They
picked their direction and ending, and figured out what would have to
happen in the last installment, right down to the last scene and line,
and what would have to happen in each book.
A further interview also describes the final scene being written during Caliban's War, but then refers to the main text rather than the epilogue:
The pair even knew Leviathan Falls’ last line — Naomi musing, “The
stars are still there. We’ll find our own way back to them” — since
they were writing the second book, Caliban’s War.
However it also includes a strong implication that Amos' fate was planned and intentionally foreshadowed early on:
In the epilogue, we learn that Amos is the one helping guide humanity
through this next stage. Why was this the right place for him to land?
Abraham: We had him refer to himself as the last man standing really
early in the series. […] He’s that combination of weird compassion and
total lack of sentimentality that it just felt right. What a great
place to grow to.