Tough Stuff is a Stunt, which by their nature are only applicable in a limited set of circumstances. Therefore should not be taken as instruction for how the general rules work. Otherwise you'd have all kinds of limitations on skills and equipment, and if Tough Stuff is considered mechanically the same as wearing Armor 1 (since you make your players specify what damage their equipment-based armor protects against), not only would anyone with a spare Refresh be foolish not to take it, but it's actually superior to wearing armor that has a rating of 1, since you never have to take the time to put it on and can never have it taken from you.
I always interpreted the comment notes from Harry, Bob and Will as suggestions for different ways to use the core information, since almost all of the notes that clarify rules are in that vein. Remember that the conceit of the DFRPG is that it's a game written by Will. So the commentary notes do not form a part of the text of the final "product" that Will is setting out to publish.
If it was intended that the core rules only allowed specific armor to protect against certain types of damage, then the rules in the armor section would state that you have to specify what each item of armor protects against.
Your rule is fine, but it's a houserule. You could also allow declarations, maneuvers and compels to represent certain armor types being ineffective against certain attacks, given suitable circumstances.