That's not what it says. It says the weakness (what this Flaw does to your magic) can be a boon:
This weakness can be a boon to a crafty character.
That's why, when you read this above you disagreed with your current stance. Yes, there are times when the Flaw doesn't limit you. But that does not explain the weakness being a boon ever. Not always being a penalty is not the same as being a boon. It's only ever a boon if Harmless Magic is useful somehow. The paragraph then goes on to show specifically how this Flaw can be a boon with an example. The only way these sentences can be true is if the example would not work without Harmless Magic.