Just a weird thing I noticed, but my Ranger is proficient in Medicine (Philosopher background), and that happens to have a higher bonus than the Herbalism kit and Nature score. It makes sense though since Nature relies on Intelligence while Medicine relies on wisdom, so I have a higher wisdom score to boost Medicine more.
However the game from the very start (lost valley campaign), would only use the Herbalism Kit bonus which is less, so as a result my crafting isn't as good as it should be.
Currently (level 12); Medicine is +8 while Herbalism/Nature is +6. Weirdly, since both Nature and Medicine grant Poisoner's Kit proficiency, it shows Medicine +6 (which it isn't it's +8), so it still seems to use the Nature/Herbalism kit bonus though showing Medicine as the skill being used.
I think the highest bonus should be used for crafting. Generally wisdom will be higher than intelligence for a ranger, so being proficient in Medicine will almost always be a better bonus than Nature/Herbalism Kit proficiency.