One of the purposes of walling thaumaturgy behind a Merit and making it specifically miracle-working (in the sense where miracle means inexplicable and not-repeatable-by-just-anyone) was to move the area of mortal competence back to something resembling mortal competence.
That is, mortals in Creation, absent Exaltation, other divine blessing, sorcerous initiation, or the thaumaturgy merit, are no more capable of working magic than they have been in real life in the past. You can brew bark to make aspirin but you can't make arbitrary healing potions or freeform potion magic as such. People in Creation can certainly try to be alchemists, and many do, but in the same sense that Creation has a lot of people who make a living as tea-readers without possessing the Read Tea Leaves Thaumaturgy Merit without even realizing they're frauds.
Now, Creation has the concept of alchemists both in the sense of "primitive chemists" and "people who seek the Philosopher's Stone," and the latter even have an established body of knowledge associated with it that e.g. an initiated sorcerer can use to suss out how to give himself those internal alchemy Merits... but without sorcerous initiation or Exaltation or something, a would-be alchemist has only slightly more chance of successfully brewing a draught of immortality as someone in the real 14th century did of using dung and crushed beetles and mirrors to turn lead into gold (that is to say, only slightly more than none, and only in the sense that there's nothing stopping you from playing a mortal sorcerer whose background is alchemical breakthrough leading to self-initiation).
That said, Creation has a bunch of stuff in it that can be used to make what would be impossible magical potion IRL, but in Creation is just... chemistry. Age-Staving Cordials. Maiden Tea. Draughts of Miraculous Health. Ghost-Flower Tea. These are probably made using an appropriate Craft, which you might as well call Craft (Alchemy). The rules for these are basically "The books have a list of potions and cordials and things and you can make those assuming you have access to appropriate ingredients as decided by the ST, and if you want to invent more, you'll need to discuss with the ST whether the existence of whatever new potion you're trying to invent is a good addition to the setting or not."
To the extent that you disagree whether removal of "basically freeform alchemist who is constantly inventing new potions but who is otherwise a pure mortal" from the setting was a good idea or not, neither the setting nor the system will assist you in finding an "officially sanctioned" "fix." The Thaumaturgy Merit doesn't mean that alchemy now falls under Craft rather than Occult; the Thaumaturgy Merit now means that "mortal alchemists" as they existed under the 2e thaumaturgy system are no longer a thing.
If you dislike this you are encouraged to house rule it. It's your game! But you're likely to grow frustrated if you seek textual evidence of one set of designer intentions when the designers are working along a different set of intentions.
