Because sometimes the groups you want at the end are exactly the groups you don't want reacting in the middle. 3,5-Dimethoxybenzaldehyde is a beautiful example.
Its aromatic ring carries two methoxy groups: -OCH3 But in many natural-product syntheses, those groups are really placeholders for something else: -OH Phenolic hydroxyl groups are important in molecules such as resveratrol-related natural products. They're also reactive.
Global Chemical Database