Toughness powers grant those "bonus" stress boxes; if the Toughness' Catch is applied, then those boxes don't apply--and if a stress larger than the now-reduced stress track is applied, the character is in danger of being taken out.
EDIT:
Example: A Malk (a fey) has four stress boxes, two normal, two from Toughness. Shooting a Malk with a lead bullet (Weapon:2) will probably just annoy it, with the second of four stress boxes full. Hitting it with an iron crowbar (Weapon:2) will fulfill the Catch, bypass the Toughness and negating those additional boxes, and seriously hurting it, filling the second of two stress boxes.