the spirit turtle in the WN got decapitated by Raphtalia, but the head keeps on regenerating so fast it doesn't stop moving unlike here. It's a bit more hectic and hard for Naofumi to get in the back on the spirit turtle in WN since it's still moving and flying monters and zombies keeps on attacking them without any rest. They would only found the japanese scripts a bit later when they start searching for a way to seal the heart of the spirit turtle. They introduced eclaire and peerless grandma a bit early here compared to WN, I'm pretty sure they introduced in WN after this arc.
in short, yes LN is a bit different compared to WN. They added more characters and events to fill the plotholes, and possibly change the ending a bit.
Edit: Added this spoiler just in case, but I can't actually called this a spoiler anymore since it has the same timeline with the WN already, but oh well, I don't want to be bothered people quoting me that this is spoiler, lol.