Alchemy requires you to put in the required mushrooms all at once and then brew it. No need to put them in the exact order.
You use the item that appears in your inventory after brewing a potion to get it's effect.
If you are trying to get True Sight, you eat the mushrooms rather than brew them.
The PC will only attempt the thirsty tree's request if you were caught by a Malice. That quest only becomes relevant once that happens.
That chest is related to the tree that wants a Lilyth mushroom. The Fragile Keys do not work. This is a hint and not the full solution.