Reynolds doesn’t have to do anything clever to lay out these apparent contradictions. He simply presents both narratives at face value. It’s up to the reader to (a) throw the book across the room in frustration and rant about its internal contradictions or (b) have faith in the author and the editor, and trust that it will all make sense eventually. Reynolds plays completely fair with the reader and gives us every chance to work out what is actually going on. And when you do work it out, it hits you with double the impact.
Through coincidence / God’s good timing [delete as applicable] I was reading the book at the same time as I found myself studying John 3:1-21 - the secret meeting between Nicodemus and Jesus. Jesus famously tells Nicodemus that “no one can see the kingdom of God unless they are born again.” I still can’t work out from Nicodemus’s reply - “How can someone be born when they are old? Surely they cannot enter a second time into their mother’s womb to be born!” - if he’s just being obtuse, or engaging in a bit of verbal jousting, challenging Jesus to come back at him.
But Jesus does come back to him, with the less ambiguous “Flesh gives birth to flesh, but the Spirit gives birth to spirit.” Okay, that seems straightforward enough. After all, they’re not the same thing, are they?
Talk about misdirection. It turns out that Jesus is only speaking generally, not specifically. More specifically - and this really shouldn't be a spoiler - on one key occasion there really was a unique union between flesh and spirit, and the result of it is the guy apparently telling Nicodemus that it can't be done. Jesus, God incarnate, uniquely brings the two together. And the incarnation is on-going. Jesus rose from the tomb in a body that was 100% physical (he could eat and drink and be touched) yet could also apparently walk through walls and closed doors and in short be wherever on earth he wanted to be. He still had that body when he rose up into heaven and there is nothing to say that he then gratefully shucked it off, job done.
Flesh and spirit were, and are still, linked through Jesus. You can just be told that, or you can have the fun of working it out for yourself.
A common mistake among writers is to put all their cards straight onto the table in the interests of being honest with their readers, and thereby reduce the impact of their story to “meh”. I think we have clearance from the top to be less straightforward, and thereby increase the impact of our tale to absolute “wow!” level.