Historically, things such as the behaviour/character of the alchemist were deemed important. To make pure metals, you were supposed to live a pure lifestyle. Which is why we talk about laboratories: laborare (working, practicing) + orare (praying, meditating).
maybe a masterful alchemical (sp?) potion gives the desired effects, while an average one does nothing. potions with no quality give opposite and adverse effects. i sorta recall (or made up) that booze has a hidden quality that affects value, something similar could be used to hide the quality of the potion. also if you use masterful ingredients (i know not all items have a quality yet), and mince/grind/chop/powder or whatever them masterfully, and blend/distill/boil (or whatever) them masterfully then you have a potion that has the desired effects. maybe the formula for a potions potency is dictated by its value, the higher the value compared with its theoretical max, the more likely it is to work.
if you combine a system like that with the formulas being unknown at the start, then the power of alchemy should be reserved only for the most persistent of fortresses, and wont unbalance gameplay early. you would have to spent lots of time playing with the formulas (or the dwarves would do this by themselves) and developing skill to actually unleash the power. maybe the alchemist could also be a noble position (like the philosopher), who works in the laboratory.
the raw ingredients for the most powerful alchemy should also be something that is not readily available at the start. im thinking elephant ears, tigers tails, giant eagle eyeballs, titan toes, (they probably don't all have to be alliterations), etc...