I have an idea on how to make Mandrakes a renewable resource while keeping their rarity.
Make Mandrakes work like normal vegetables, that is that you get a seed when you feed one to a bird. Also maybe make them coughable by Catcoons. Very rare chance ofc.
And how to make them farmable but still very rare and difficult to obtain in large quantities?
Make them only be able to grow during a full moon.
That way you can always make a Pan Flute or Mandrake Soup more than 5 times during the game while it won't become something you can just eat all the time.
Remember that birds sleep during night so you won't be able to mass produce them during one night by applying manure and feeding them to a bird instantly. It will take in game months to be able to get enough seeds to make a reliable large scale farm.