Bakers percentages (measuring by-weight as a percentage of the largest mass ingredient (usually flour or water)) only work for lean dough and only for the non-fermenting components of that dough.
Put more concretely, one does not linearly scale the yeast in a lean dough. It results in far too rapid a fermentation, over-proofed dough, and less flavor complexity.
Cooking is stacking exponents with whole range of parameters, so linear scaling indeed happens only sometimes, if you squint hard :). Unfortunately, the error bars on everything are huge - purity and quantity of ingredients, accuracy of measuring devices, accuracy and reliability of equipment, and people's care about the process - they're all so bad that cooking simply cannot be anything better than an art.
(The non-art variant is called process engineering.)
But yeah, it is the messiness and art of it that keeps it fun for me (especially after a day of math and coding)!