There is a significant difference between having established rules, and having perfectly known rules. Mythological magic had rules, and nobody ever claimed that wasn't very magical. Whether you are talking about old school totem invocations and their resultant taboos and banes, or the mathematics of hermetic magic, or even priests invoking gods and saints(different archangels providing different boons, though apparently most demons provide access to the future and sex) for effect. Rules make the difference between 'its magic' and 'one guy making shit up', repeating a given ritual and its conditions gives you the same effect, or magic cannot be taught.
Magi also take various components of magic and extrapolate further effects. Say sulfur is associated with fire, and thus purification, so an elixir made with sulfur would be effective at banishing unwanted influences, cleaning, creating fire or warding off disease, but be unlikely to aid in creating water, transforming one thing into another, flying or making metal harder.
Spellcraft especially, implies magic, and especially invoked magic(i.e. spells and items) are distinct, with analyzable effects and predictable outcomes, even in setting. You can look at the spell components as a mage casts and know with reasonable certainty whats going to come out is a fireball and not a fiendish rabbit.
More importantly, it gives at least a similar degree of restriction to what can or cannot be done in the world as physical actions, if restricted along different lines. It provides a schema for such actions across the magic/mundane medium, since you can now relate magical actions to the setting and adjudicate. It does not also necessarily mean you have a Grand Unified Theory for magic, different effects might only follow a smaller number of universal rules. This is useful for consistency across the system and within magic itself.
How do you affect a target you can't see or touch. Its also useful for obtaining defenses and countermeasures against magic other than direct applications of magic. Can you confiscate only the spell components and foci needed for destructive magic without preventing a mage from plying his trade entirely? What are the mundane means of telling that someone is a transformed faerie rather than an actual prince? If magic flows across the world, would a scholar be able to study and identify areas of particularly intense or weak magic, or where natural portals are likely to form? Can this energy be cut off or manipulated by mundane means?
