The rule was written before anyone used boxes. It was, and still is, the shadow of the plates upon the car structure. Per Ryan MIles @ SCCA tech 8/9/12.
The 15 in(?) longest side rule counts.
Basically if you make a crush box, place it on a 12x12 plate , you are good to go. As the rule is written today and clarified by SCCA tech.

Maybe the crush box needs a max side size also. As long as they are less than the 15 in rule, up the sill plate, they should be very safe.
I am sure that if you built a fancy box over about 6in from the floor plate/level , you may have some valid safety issues.
You should avoid the potential to crush the box more than you have room to the roof, minus 2in, IMHO. I like 1/2 to 3/4 in before it all loads up .
Short story is that there is very little stiffness gain, as long as the cage sits inside of the 12x12 rule. (Not much even as the cage gets really tied, either.)