It was consistent AFAIR, though it dropped at least once during that book. For those who haven't read (spoiler), the "spaceship speed limit" refers to a particular region of artificial space, where there was an alien object whose defense mechanisms involved capturing everything moving faster than a set limit relative to it. That limit was adjusted by the object based on perceived danger, and if you happened to cross it, you'd be slowed down without any regard to what sudden high deceleration does to you.

Personally, I liked the protomolecule stuff, and my biggest complain was that there's so little of it in the books. 90% of the writing involves bog-standard real physics, and the protomolecule trickery only shows up occasionally.