If you think about it, there are actually two endings to the book. The last chapter ends Manjiro's story as Preus has written it, and then the Epilogue comes along and wraps up all the factual loose ends about Manjiro's life.
Preus's rendering of Manjiro's life ends on an uncertain note. On the last page of the last chapter, we learn that Manjiro is supposed to go see the "great lord of Tosa" in Kochi. The messenger doesn't really know why, but rumor has it that there are two possibilities: Manjiro's in big trouble and might be imprisoned on spy charges again (5.41.13), or he's being summoned to teach the samurai about Americans (5.41.15).
Which is it? Spy or samurai? Who can tell? The last chapter leaves us with is Manjiro's own calm faith and hope in himself:
Within him, Manjiro knew, beat a heart scoured by sand, pounded by waves, burned by sun, and polished by rain and wind. It would always be a simple heart of a fisherman, but perhaps it had also become the mighty heart of a samurai. (5.41.18)
So while the Epilogue follows and answers the question about what happens next to Manjiro, Preus's story ends by highlighting who he is inside—his heart, calm, and strength.