FYI: in the rules, "armor against physical stress" is "armor against physical stress." So if you have Inhuman Toughness with a Catch of "Silver" then it still gives you Armor: 1 against magic that would inflict physical stress. However Silver would be a +2 catch for a were-form or a +1 for anyone other type. But most important about a silver catch is that your armor (from Inhuman Toughness) would apply to magical attacks.
A Catch of "Magic" on toughness just means your Armor or Recovery won't apply when you are targeted by magic. Remember Toughness powers only apply to Physical Stress. I haven't seen any Mental or Social toughness powers.
Inhuman Recovery is pretty awesome. Getting rid of Mild Physical Consequences along with your dots of Physical Stress is handy.
Would a catch of magic be a +1 or +2? I am trying to think of a template that makes sense for a catch of magic. Only one seems to be the very open ended Emissary of Power. I think the best way to determine the second bullet point on the cost list is to imagine if the question were posed to a person that was in the dark about magic existing and were asked what they think the catch would be, if they got it on the early guesses, it is a +2, else it is a +1 (unless it is a case of "You have to make him swallow a mushroom stuffed in your wet left sock, which you dipped in an eastern running river with the first rays of dawn shining on the act"). But I seriously can't imagine a monster that falls under the "Duh, use magic" header.