Here's the thing - it doesn't specifically mention Health. Neither does Chopper's unique.
Zeb's unique, on the other hand, does. "Zeb has bonus Max Protection equal to +40% of his Max Health..."
Even his recovery simply states, "...recovers 15% Protection...".No mention of Health.
That being said, a quick test with Enfys does SEEM to bear out the idea that the boost is based off of health, not protection. With 8k health and 9k prot, she recovered a bit. With 7k health and 1500 prot, the recovery seemed to be larger than her initial base protection (based on the number/size of prot bars present).
Is this definitive proof? Of course not. Am I suddenly going to stack Enfys with health? Nope. I even took all the max prot mods off in favor of utilizing her whole kit instead of going all in on a feature I hope to not even need that much.