Even with the large boxes, the body can still be warped!
I got the first go round of this kit years ago (blue car box art) and the roof was bent right at the C pillar. I think sometimes they don't let the body cool down long enough, and the contents of the other items in the box puts too much pressure on a still too warm body.
HAH, it's funny you mention that, Bill - just remembered the very kit that got me honing the just-off-boiling-water technique was in fact Monogram's first-issue, metallic blue '59 Impala in that same big box. Body was twisted up like a braid, but I managed to flatten it out.