Actually, Type III or "hard" anodizing does change the fundamental toughness of the underlying substrate, in this case aluminum. Type III is a more complicated and aggressive means of creating a thicker oxide layer that actually makes the part stronger. For example, aluminum handgun frames are hard-anodized to make the frame more resistant to the metal fatigue that a firearm is subject to.
Based on current anectodal evidence (everyone seems to be getting little nicks and scratches on the anodized iP5 parts, including me), I would guess that Apple did not spec in hard anodizing. The softer "decorative" anodizing might be acceptable in a lesser product, but Apple's flagship smartphone? A point or two off, big A.