You may accidentally wish something you don’t yet know the true nature of, and this will create a fragile mess at the bottom. It usually does, cause algorithmic nature of things is rarely intuitive. Starting from the bottom is like starting from quarks that you have rather than from “I want magic to exist”. Well it does not. You reach the bottom and there’s quarks instead of magicules and you’ve lost all context clues on the way which could help to convert between two physics.
Both approaches have their use, because sometimes you have to be bold with your wishes to solve a deep problem. But personally I prefer magic to be packed into the before-topmost layer. I.e. build from the bottom up, and then, just before the business logic, create a convenience magic layer that translates to/from business speak. It becomes adjustable and doesn’t induce a tangled mess all the way down.