As I understand it, substances will have different effects depending on how they are applied. So, a substance that might have a medicinal use if applied topically could be a toxic poison if ingested.
And I am sure the devs, looking over your question of which skills would be involved, would say, "yes." That is, all those skills would be involved -- possibly in combination, possibly sequentially. So, an apothecary might need an ingredient prepared by a skilled alchemist who used ingredients from a skilled herbalist.
I imagine that people will go around the world asking "delectable tea or deadly poison?" And sometimes the answer, like the answer to the skills, will be "yes."