I guess I'm lucky. I have bought 3 Manix XL's from KW. Two s90v's and one s30v.Not one problem with the way they packed or shipped with any of them. All Spyderco boxes where in great shape. KnifeWorks is always my first go too online vender when looking for a new knife.
You're definitely lucky. Spyderco should probably look into getting more appropriate boxes- more of my Spyderco boxes have some kind of tear or defect than those that do not, but in this case the knife tore both sides of the inner box and was starting to slide out of the Spyderco box (it never got its shot at the USPS small flat rate lol).

It wouldn't bother me one bit (blasphemy!!) aside from the resale value and the fact that if I sell it (which I did), that person doesn't get a good box if that is a big deal for them - people love their boxes, and when selling this one I figured it was on me to show the damage of the box as much as it was to show if any damage was on the knife itself.
I don't think Knifeworks is totally free of fault though - it's obvious that these are stout knives in flimsy boxes, and it's fairly well known that people want the boxes with the knife (I would think moreso with dealer exclusives). Pack for shipping accordingly.