No it doesn't. The catch bypasses your Armor and extra boxes, so you'll either looke like this:
(00)000X plus consequences or this:
000X(00) plus consequences.
thinking about it, this is what I don't like about it:
Let's say you have toughness (0000)0000
and lets say you take a 1shift hit; a 3 shift hit and a 4 shift hit (after armour is applied)
your box looks like this: (X0XX)0000
Now, you get hit by a catch satisfying, 3 shift hit
You get to take that hit with a free box (X0XX)00X0 because the first 4 boxes no longer count.
Doing it this way gives you extra 1-4 shift hits.
If you did it the other way
0000(0000)
your 3 hits would look like this:
X0XX(0000)
the catch satisfying 3-shift hit would have to roll over to a consequence (since it can't roll over to your toughness boxes), whereas with your method, you'd still get to soak it. Technically, you can only soak each box once - not twice.