Granted, Toughness doing something is a benefit - it represents the difference between a scrawny, malnourished beggar and a healthy, trained warrior when it comes to resisting the effects of injury.
Whether this should actually make a difference when it comes to such terrible weapons as futuristic laser rifles that flash-boil your limbs, or armour-piercing miniature rocket that explode inside your body is, of course, something else to consider.*
And then, naturally, it having operate as a simple soak like armour is not the only way this could be represented.
tl;dr - I'm definitively in favour of keeping Toughness having an effect on resilience, but I'm ardently opposed to it having this effect.
*: quick idea - as yet another possible alternative, perhaps TB should only apply for damage from Primitive weapons?